From c3b594c214ad93407d24a82f9552568b6588ca08 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 14 Aug 2023 23:59:09 -0400
Subject: [PATCH 01/12] Testing

Yarn upgrade

Misc

Human vs mouse example

Misc

Misc

Updates

Misc

Misc
---
 .../src/BedTabixAdapter/BedTabixAdapter.ts    |   4 +-
 plugins/comparative-adapters/package.json     |   1 +
 .../src/PAFAdapter/PAFAdapter.ts              |  15 +-
 .../src/PAFAdapter/util.ts                    |  63 --------
 .../PairwiseIndexedPAFAdapter.ts              | 134 ++++++++++++++++++
 .../PairwiseIndexedPAFAdapter/configSchema.ts |  72 ++++++++++
 .../src/PairwiseIndexedPAFAdapter/index.ts    |  19 +++
 .../index.ts}                                 |   0
 plugins/comparative-adapters/src/index.ts     |  12 +-
 .../src/{PAFAdapter => }/util.test.ts         |   0
 plugins/comparative-adapters/src/util.ts      |  63 ++++++++
 .../components/LinearSyntenyRendering.tsx     |  24 ++--
 .../wiggle/src/BigWigAdapter/BigWigAdapter.ts |   6 +-
 .../src/components/NoConfigMessage.tsx        |   2 +-
 .../config.json}                              |  29 ++++
 15 files changed, 349 insertions(+), 95 deletions(-)
 create mode 100644 plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
 create mode 100644 plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
 create mode 100644 plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts
 rename plugins/comparative-adapters/src/{PAFAdapter/SyntenyFeature.ts => SyntenyFeature/index.ts} (100%)
 rename plugins/comparative-adapters/src/{PAFAdapter => }/util.test.ts (100%)
 rename test_data/{human_vs_mouse.json => hs1_vs_mm39/config.json} (75%)

diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
index 097e463326..c6a4edd182 100644
--- a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
+++ b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
@@ -7,11 +7,13 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { FileLocation, Region, Feature } from '@jbrowse/core/util'
 import { TabixIndexedFile } from '@gmod/tabix'
-import { featureData } from '../util'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
+// locals
+import { featureData } from '../util'
+
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
   private parser: BED
 
diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json
index 8581d5dd5d..01b414841a 100644
--- a/plugins/comparative-adapters/package.json
+++ b/plugins/comparative-adapters/package.json
@@ -37,6 +37,7 @@
   },
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.3",
+    "@gmod/tabix": "^1.5.6",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
diff --git a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
index bafbafcdc7..ee76e3462a 100644
--- a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
@@ -15,15 +15,15 @@ import { unzip } from '@gmod/bgzf-filehandle'
 import { MismatchParser } from '@jbrowse/plugin-alignments'
 
 // locals
-import SyntenyFeature from './SyntenyFeature'
-import { isGzip, parseLineByLine } from '../util'
+import SyntenyFeature from '../SyntenyFeature'
 import {
-  getWeightedMeans,
   flipCigar,
   swapIndelCigar,
   parsePAFLine,
-  PAFRecord,
-} from './util'
+  isGzip,
+  parseLineByLine,
+} from '../util'
+import { getWeightedMeans, PAFRecord } from './util'
 
 const { parseCigar } = MismatchParser
 
@@ -102,8 +102,9 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
 
       // The index of the assembly name in the query list corresponds to the
       // adapter in the subadapters list
-      const index = assemblyNames.indexOf(query.assemblyName)
       const { start: qstart, end: qend, refName: qref, assemblyName } = query
+      const index = assemblyNames.indexOf(assemblyName)
+      const flip = index === 0
       if (index === -1) {
         console.warn(`${assemblyName} not found in this adapter`)
         observer.complete()
@@ -117,8 +118,6 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
         let mateName = ''
         let mateStart = 0
         let mateEnd = 0
-        const flip = index === 0
-        const assemblyName = assemblyNames[+!flip]
         if (index === 0) {
           start = r.qstart
           end = r.qend
diff --git a/plugins/comparative-adapters/src/PAFAdapter/util.ts b/plugins/comparative-adapters/src/PAFAdapter/util.ts
index 4faad3cc5a..0499f095c4 100644
--- a/plugins/comparative-adapters/src/PAFAdapter/util.ts
+++ b/plugins/comparative-adapters/src/PAFAdapter/util.ts
@@ -107,66 +107,3 @@ function weightedMean(tuples: [number, number][]) {
   )
   return valueSum / weightSum
 }
-
-export function parsePAFLine(line: string) {
-  const [
-    qname,
-    ,
-    qstart,
-    qend,
-    strand,
-    tname,
-    ,
-    tstart,
-    tend,
-    numMatches,
-    blockLen,
-    mappingQual,
-    ...fields
-  ] = line.split('\t')
-
-  const rest = Object.fromEntries(
-    fields.map(field => {
-      const r = field.indexOf(':')
-      const fieldName = field.slice(0, r)
-      const fieldValue = field.slice(r + 3)
-      return [fieldName, fieldValue]
-    }),
-  )
-
-  return {
-    tname,
-    tstart: +tstart,
-    tend: +tend,
-    qname,
-    qstart: +qstart,
-    qend: +qend,
-    strand: strand === '-' ? -1 : 1,
-    extra: {
-      numMatches: +numMatches,
-      blockLen: +blockLen,
-      mappingQual: +mappingQual,
-      ...rest,
-    },
-  } as PAFRecord
-}
-
-export function flipCigar(cigar: string[]) {
-  const arr = []
-  for (let i = cigar.length - 2; i >= 0; i -= 2) {
-    arr.push(cigar[i])
-    const op = cigar[i + 1]
-    if (op === 'D') {
-      arr.push('I')
-    } else if (op === 'I') {
-      arr.push('D')
-    } else {
-      arr.push(op)
-    }
-  }
-  return arr
-}
-
-export function swapIndelCigar(cigar: string) {
-  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
-}
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
new file mode 100644
index 0000000000..47d97bdcbe
--- /dev/null
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
@@ -0,0 +1,134 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { FileLocation, Region } from '@jbrowse/core/util/types'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { Feature } from '@jbrowse/core/util'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { openLocation } from '@jbrowse/core/util/io'
+import { TabixIndexedFile } from '@gmod/tabix'
+
+// locals
+import { parsePAFLine } from '../util'
+import SyntenyFeature from '../SyntenyFeature'
+
+interface PAFOptions extends BaseOptions {
+  config?: AnyConfigurationModel
+}
+
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  protected paf: TabixIndexedFile
+
+  public constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
+    const pafGzLoc = this.getConf('pafGzLocation') as FileLocation
+    const type = this.getConf(['index', 'indexType'])
+    const loc = this.getConf(['index', 'location'])
+    const pm = this.pluginManager
+
+    this.paf = new TabixIndexedFile({
+      filehandle: openLocation(pafGzLoc, pm),
+      csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
+      tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
+      chunkCacheSize: 50 * 2 ** 20,
+    })
+  }
+  async getHeader() {
+    return this.paf.getHeader()
+  }
+
+  getAssemblyNames(): string[] {
+    const assemblyNames = this.getConf('assemblyNames') as string[]
+    if (assemblyNames.length === 0) {
+      return [
+        this.getConf('queryAssembly') as string,
+        this.getConf('targetAssembly') as string,
+      ]
+    }
+    return assemblyNames
+  }
+
+  public async hasDataForRefName() {
+    return true
+  }
+
+  async getRefNames(opts: BaseOptions & { regions?: Region[] } = {}) {
+    const r1 = opts.regions?.[0].assemblyName
+    if (!r1) {
+      throw new Error('no assembly name provided')
+    }
+
+    const idx = this.getAssemblyNames().indexOf(r1)
+    const names = await this.paf.getReferenceSequenceNames(opts)
+    if (idx === 0) {
+      return names.filter(n => n.startsWith('q')).map(n => n.slice(1))
+    } else if (idx === 1) {
+      return names.filter(n => n.startsWith('t')).map(n => n.slice(1))
+    }
+    return []
+  }
+
+  getFeatures(query: Region, opts: PAFOptions = {}) {
+    return ObservableCreate<Feature>(async observer => {
+      const { assemblyName } = query
+
+      const assemblyNames = this.getAssemblyNames()
+      const index = assemblyNames.indexOf(assemblyName)
+      const flip = index === 0
+      const letter = flip ? 't' : 'q'
+
+      await this.paf.getLines(letter + query.refName, query.start, query.end, {
+        lineCallback: (line, fileOffset) => {
+          const r = parsePAFLine(line)
+          const refName = r.qname.slice(1)
+          const start = r.qstart
+          const end = r.qend
+          const mateName = r.tname
+          const mateStart = r.tstart
+          const mateEnd = r.tend
+
+          const { extra, strand } = r
+          const { numMatches = 0, blockLen = 1, cg, ...rest } = extra
+
+          observer.next(
+            new SyntenyFeature({
+              uniqueId: fileOffset + assemblyName,
+              assemblyName,
+              start,
+              end,
+              type: 'match',
+              refName,
+              strand,
+              ...rest,
+              CIGAR: extra.cg,
+              syntenyId: fileOffset,
+              identity: numMatches / blockLen,
+              numMatches,
+              blockLen,
+              mate: {
+                start: mateStart,
+                end: mateEnd,
+                refName: mateName,
+                assemblyName: assemblyNames[+flip],
+              },
+            }),
+          )
+        },
+        signal: opts.signal,
+      })
+
+      observer.complete()
+    })
+  }
+
+  freeResources(/* { query } */): void {}
+}
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
new file mode 100644
index 0000000000..a585dc67cd
--- /dev/null
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
@@ -0,0 +1,72 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { types } from 'mobx-state-tree'
+
+/**
+ * #config PairwiseIndexedPAFAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const PairwiseIndexedPAFAdapter = ConfigurationSchema(
+  'PairwiseIndexedPAFAdapter',
+  {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+      type: 'stringArray',
+      defaultValue: [],
+      description:
+        'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
+    },
+    /**
+     * #slot
+     */
+    targetAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames: the target assembly name',
+    },
+    /**
+     * #slot
+     */
+    queryAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames: the query assembly name',
+    },
+    /**
+     * #slot
+     */
+    pafGzLocation: {
+      type: 'fileLocation',
+      description: 'location of pairwise tabix indexed PAF',
+      defaultValue: { uri: '/path/to/data/file.paf.gz' },
+    },
+    /**
+     * #slot
+     */
+    index: ConfigurationSchema('TabixIndex', {
+      /**
+       * #slot index.indexType
+       */
+      indexType: {
+        model: types.enumeration('IndexType', ['TBI', 'CSI']),
+        type: 'stringEnum',
+        defaultValue: 'TBI',
+      },
+      /**
+       * #slot index.location
+       */
+      location: {
+        type: 'fileLocation',
+        defaultValue: {
+          uri: '/path/to/my.paf.gz.tbi',
+          locationType: 'UriLocation',
+        },
+      },
+    }),
+  },
+  { explicitlyTyped: true },
+)
+
+export default PairwiseIndexedPAFAdapter
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts
new file mode 100644
index 0000000000..90aebd5d21
--- /dev/null
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts
@@ -0,0 +1,19 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'PairwiseIndexedPAFAdapter',
+        displayName: 'Pairwise indexed PAF adapter',
+        configSchema,
+        adapterMetadata: {
+          hiddenFromGUI: true,
+        },
+        getAdapterClass: () =>
+          import('./PairwiseIndexedPAFAdapter').then(r => r.default),
+      }),
+  )
+}
diff --git a/plugins/comparative-adapters/src/PAFAdapter/SyntenyFeature.ts b/plugins/comparative-adapters/src/SyntenyFeature/index.ts
similarity index 100%
rename from plugins/comparative-adapters/src/PAFAdapter/SyntenyFeature.ts
rename to plugins/comparative-adapters/src/SyntenyFeature/index.ts
diff --git a/plugins/comparative-adapters/src/index.ts b/plugins/comparative-adapters/src/index.ts
index 451ab31975..98a98d780d 100644
--- a/plugins/comparative-adapters/src/index.ts
+++ b/plugins/comparative-adapters/src/index.ts
@@ -3,6 +3,7 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import { FileLocation } from '@jbrowse/core/util/types'
 
 import PAFAdapterF from './PAFAdapter'
+import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter'
 import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter'
 import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter'
 import MashMapAdapterF from './MashMapAdapter'
@@ -20,6 +21,7 @@ export default class ComparativeAdaptersPlugin extends Plugin {
 
   install(pluginManager: PluginManager) {
     PAFAdapterF(pluginManager)
+    PairwiseIndexedPAFAdapterF(pluginManager)
     DeltaAdapterF(pluginManager)
     ChainAdapterF(pluginManager)
     MCScanAnchorsAdapterF(pluginManager)
@@ -50,12 +52,10 @@ export default class ComparativeAdaptersPlugin extends Plugin {
     pluginManager.addToExtensionPoint(
       'Core-guessTrackTypeForLocation',
       (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'PAFAdapter') {
-            return 'SyntenyTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
+        return (adapterName: string) =>
+          adapterName === 'PAFAdapter'
+            ? 'SyntenyTrack'
+            : trackTypeGuesser(adapterName)
       },
     )
   }
diff --git a/plugins/comparative-adapters/src/PAFAdapter/util.test.ts b/plugins/comparative-adapters/src/util.test.ts
similarity index 100%
rename from plugins/comparative-adapters/src/PAFAdapter/util.test.ts
rename to plugins/comparative-adapters/src/util.test.ts
diff --git a/plugins/comparative-adapters/src/util.ts b/plugins/comparative-adapters/src/util.ts
index 35429811c1..fc68943d05 100644
--- a/plugins/comparative-adapters/src/util.ts
+++ b/plugins/comparative-adapters/src/util.ts
@@ -64,3 +64,66 @@ export function parseLineByLine(
   }
   return entries
 }
+
+export function parsePAFLine(line: string) {
+  const [
+    qname,
+    ,
+    qstart,
+    qend,
+    strand,
+    tname,
+    ,
+    tstart,
+    tend,
+    numMatches,
+    blockLen,
+    mappingQual,
+    ...fields
+  ] = line.split('\t')
+
+  const rest = Object.fromEntries(
+    fields.map(field => {
+      const r = field.indexOf(':')
+      const fieldName = field.slice(0, r)
+      const fieldValue = field.slice(r + 3)
+      return [fieldName, fieldValue]
+    }),
+  )
+
+  return {
+    tname,
+    tstart: +tstart,
+    tend: +tend,
+    qname,
+    qstart: +qstart,
+    qend: +qend,
+    strand: strand === '-' ? -1 : 1,
+    extra: {
+      numMatches: +numMatches,
+      blockLen: +blockLen,
+      mappingQual: +mappingQual,
+      ...rest,
+    },
+  } as PAFRecord
+}
+
+export function flipCigar(cigar: string[]) {
+  const arr = []
+  for (let i = cigar.length - 2; i >= 0; i -= 2) {
+    arr.push(cigar[i])
+    const op = cigar[i + 1]
+    if (op === 'D') {
+      arr.push('I')
+    } else if (op === 'I') {
+      arr.push('D')
+    } else {
+      arr.push(op)
+    }
+  }
+  return arr
+}
+
+export function swapIndelCigar(cigar: string) {
+  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
+}
diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx
index 1655e218a3..0bdfc02b9a 100644
--- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx
+++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx
@@ -136,6 +136,7 @@ const LinearSyntenyRendering = observer(function ({
             const f2 = f1.mate
             const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)
             const cigarIdx = getId(r2, g2, b2, unitMultiplier2)
+            const cigarOp = cigar[cigarIdx]
             const l1 = f1.end - f1.start
             const l2 = f2.end - f2.start
             const identity = f1.identity
@@ -145,22 +146,17 @@ const LinearSyntenyRendering = observer(function ({
               `Loc1: ${assembleLocString(f1)}`,
               `Loc2: ${assembleLocString(f2)}`,
               `Inverted: ${f1.strand === -1}`,
-              `Query len: ${l1}`,
-              `Target len: ${l2}`,
+              `Query len: ${l1.toLocaleString('en-US')}`,
+              `Target len: ${l2.toLocaleString('en-US')}`,
+              identity ? `Identity: ${identity.toPrecision(2)}` : '',
+              cigarOp ? `CIGAR operator: ${cigarOp}${cigar[cigarIdx + 1]}` : '',
+              n1 ? `Name 1: ${n1}` : '',
+              n2 ? `Name 1: ${n2}` : '',
             ]
-            if (identity) {
-              tooltip.push(`Identity: ${identity}`)
-            }
+              .filter(f => !!f)
+              .join('<br/>')
 
-            if (cigar[cigarIdx]) {
-              tooltip.push(
-                `CIGAR operator: ${cigar[cigarIdx]}${cigar[cigarIdx + 1]}`,
-              )
-            }
-            if (n1 && n2) {
-              tooltip.push(`Name 1: ${n1}`, `Name 2: ${n2}`)
-            }
-            setTooltip(tooltip.join('<br/>'))
+            setTooltip(tooltip)
           }
         }}
         onMouseLeave={() => model.setMouseoverId(undefined)}
diff --git a/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts b/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts
index c9dedbccc6..9229dc8984 100644
--- a/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts
+++ b/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts
@@ -17,8 +17,10 @@ interface WiggleOptions extends BaseOptions {
 }
 
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private setupP?: Promise<{ bigwig: BigWig; header: any }>
+  private setupP?: Promise<{
+    bigwig: BigWig
+    header: Awaited<ReturnType<BigWig['getHeader']>>
+  }>
 
   public static capabilities = [
     'hasResolution',
diff --git a/products/jbrowse-web/src/components/NoConfigMessage.tsx b/products/jbrowse-web/src/components/NoConfigMessage.tsx
index 176cba7870..f883d2071d 100644
--- a/products/jbrowse-web/src/components/NoConfigMessage.tsx
+++ b/products/jbrowse-web/src/components/NoConfigMessage.tsx
@@ -9,7 +9,7 @@ export default function NoConfigMessage() {
     ['test_data/breakpoint/config.json', 'Breakpoint'],
     ['test_data/config_dotplot.json', 'Grape/Peach dotplot'],
     ['test_data/config_synteny_grape_peach.json', 'Grape/Peach synteny'],
-    ['test_data/human_vs_mouse.json', 'Human vs mouse synteny'],
+    ['test_data/hs1_vs_mm39/config.json', 'Hs1 vs mm39 synteny'],
     ['test_data/yeast_synteny/config.json', 'Yeast synteny'],
     ['test_data/config_many_contigs.json', 'Many contigs'],
     ['test_data/config_honeybee.json', 'Honeybee'],
diff --git a/test_data/human_vs_mouse.json b/test_data/hs1_vs_mm39/config.json
similarity index 75%
rename from test_data/human_vs_mouse.json
rename to test_data/hs1_vs_mm39/config.json
index 099d482a72..8b31c9381c 100644
--- a/test_data/human_vs_mouse.json
+++ b/test_data/hs1_vs_mm39/config.json
@@ -14,6 +14,15 @@
             "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt"
           }
         }
+      },
+      "refNameAliases": {
+        "adapter": {
+          "type": "RefNameAliasAdapter",
+          "location": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt",
+            "locationType": "UriLocation"
+          }
+        }
       }
     },
     {
@@ -95,6 +104,26 @@
         "queryAssembly": "mm39"
       },
       "assemblyNames": ["hs1", "mm39"]
+    },
+    {
+      "type": "SyntenyTrack",
+      "trackId": "liftover_pairwise_paf",
+      "name": "liftover_pairwise_paf",
+      "adapter": {
+        "type": "PairwiseIndexedPAFAdapter",
+        "pafGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1_vs_mm39.paf.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1_vs_mm39.paf.gz.tbi"
+          }
+        },
+
+        "targetAssembly": "hs1",
+        "queryAssembly": "mm39"
+      },
+      "assemblyNames": ["hs1", "mm39"]
     }
   ]
 }

From 66e372f2a6ae6da6704fa93862f35aa8c59beeca Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Fri, 8 Sep 2023 15:25:20 -0400
Subject: [PATCH 02/12] Add jbrowse CLI command process-paf

---
 .../src/commands/process-paf.test.ts          | 19 ++++
 .../jbrowse-cli/src/commands/process-paf.ts   | 91 +++++++++++++++++++
 2 files changed, 110 insertions(+)
 create mode 100644 products/jbrowse-cli/src/commands/process-paf.test.ts
 create mode 100644 products/jbrowse-cli/src/commands/process-paf.ts

diff --git a/products/jbrowse-cli/src/commands/process-paf.test.ts b/products/jbrowse-cli/src/commands/process-paf.test.ts
new file mode 100644
index 0000000000..a1e91f4d78
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/process-paf.test.ts
@@ -0,0 +1,19 @@
+/**
+ * @jest-environment node
+ */
+
+import path from 'path'
+
+import { setup } from '../testUtil'
+
+const base = path.join(__dirname, '..', '..', 'test', 'data')
+const simplePaf = path.join(base, 'volvox_inv_indels.paf')
+const testConfig = path.join(base, 'test_config.json')
+
+describe('process-paf', () => {
+  setup
+    .command(['process-paf', simplePaf])
+    .it('fails if load flag isnt passed in for a localFile', ctx => {
+      console.log(ctx.stdoutWrite)
+    })
+})
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/process-paf.ts
new file mode 100644
index 0000000000..d4ebe8b8af
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/process-paf.ts
@@ -0,0 +1,91 @@
+import fs from 'fs'
+import JBrowseCommand from '../base'
+
+import readline from 'readline'
+import { createGunzip } from 'zlib'
+
+function getReadline(filename: string) {
+  const stream = fs.createReadStream(filename)
+  return readline.createInterface({
+    input: filename.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
+  })
+}
+
+const cigarRegex = new RegExp(/([MIDNSHPX=])/)
+
+export function parseCigar(cigar = '') {
+  return cigar.split(cigarRegex).slice(0, -1)
+}
+export function flipCigar(cigar: string[]) {
+  const arr = []
+  for (let i = cigar.length - 2; i >= 0; i -= 2) {
+    arr.push(cigar[i])
+    const op = cigar[i + 1]
+    if (op === 'D') {
+      arr.push('I')
+    } else if (op === 'I') {
+      arr.push('D')
+    } else {
+      arr.push(op)
+    }
+  }
+  return arr
+}
+
+export function swapIndelCigar(cigar: string) {
+  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
+}
+
+export default class ProcessPAF extends JBrowseCommand {
+  // @ts-expect-error
+  target: string
+
+  static description = 'Pairwise index the PAF'
+
+  static examples = [
+    '# processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF',
+    '$ jbrowse process-paf file.paf > output.ppaf',
+  ]
+
+  static args = [
+    {
+      name: 'track',
+      required: true,
+      description: `Track file or URL`,
+    },
+  ]
+
+  async run() {
+    const { args: runArgs } = this.parse(ProcessPAF)
+
+    const { track: filename } = runArgs
+
+    const rl1 = getReadline(filename)
+    for await (const line of rl1) {
+      // eslint-disable-next-line no-console
+      console.log(`q${line}`)
+    }
+    rl1.close()
+
+    const rl2 = getReadline(filename)
+    for await (const line of rl2) {
+      const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
+      const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
+
+      const CIGAR = rest[cigarIdx]
+      if (CIGAR) {
+        rest[cigarIdx] = `cg:Z:${
+          strand === '-'
+            ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
+            : swapIndelCigar(CIGAR.slice(5))
+        }`
+      }
+
+      // eslint-disable-next-line no-console
+      console.log(
+        [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t'),
+      )
+    }
+    rl2.close()
+  }
+}

From 30e63969bffe52a123df706dd76c60b7c455bd7a Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Fri, 8 Sep 2023 15:28:51 -0400
Subject: [PATCH 03/12] [skip ci] Update snaps

---
 .../__snapshots__/process-paf.test.ts.snap    | 21 +++++++++++++++++++
 .../src/commands/process-paf.test.ts          | 14 +++++++------
 .../jbrowse-cli/src/commands/process-paf.ts   |  6 ++----
 3 files changed, 31 insertions(+), 10 deletions(-)
 create mode 100644 products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap

diff --git a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
new file mode 100644
index 0000000000..660db3ad5a
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
@@ -0,0 +1,21 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`process-paf processes volvox paf 1`] = `15`;
+
+exports[`process-paf processes volvox paf 2`] = `
+"qctgA	49186	26805	49184	+	ctgA	50001	27258	50001	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2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+tctgA	50001	18559	19001	-	ctgA	49186	18309	18754	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:17M2D15M1D18M1I27M1D10M2D9M1D26M7I19M1D7M2I52M1I33M1I56M1D7M1D18M1I11M8D14M1I2M2I13M1I20M1I30M2D15M1D5M
+tctgA	50001	1859	2192	-	ctgA	49186	1860	2214	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
+"
+`;
diff --git a/products/jbrowse-cli/src/commands/process-paf.test.ts b/products/jbrowse-cli/src/commands/process-paf.test.ts
index a1e91f4d78..dac2e56686 100644
--- a/products/jbrowse-cli/src/commands/process-paf.test.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.test.ts
@@ -8,12 +8,14 @@ import { setup } from '../testUtil'
 
 const base = path.join(__dirname, '..', '..', 'test', 'data')
 const simplePaf = path.join(base, 'volvox_inv_indels.paf')
-const testConfig = path.join(base, 'test_config.json')
 
 describe('process-paf', () => {
-  setup
-    .command(['process-paf', simplePaf])
-    .it('fails if load flag isnt passed in for a localFile', ctx => {
-      console.log(ctx.stdoutWrite)
-    })
+  setup.command(['process-paf', simplePaf]).it('processes volvox paf', ctx => {
+    let res = ''
+    for (const obj of ctx.stdoutWrite.mock.calls) {
+      res += obj[0]
+    }
+    expect(res.split('\n').length).toMatchSnapshot()
+    expect(res).toMatchSnapshot()
+  })
 })
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/process-paf.ts
index d4ebe8b8af..154011a82f 100644
--- a/products/jbrowse-cli/src/commands/process-paf.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.ts
@@ -62,8 +62,7 @@ export default class ProcessPAF extends JBrowseCommand {
 
     const rl1 = getReadline(filename)
     for await (const line of rl1) {
-      // eslint-disable-next-line no-console
-      console.log(`q${line}`)
+      this.log(`q${line}`)
     }
     rl1.close()
 
@@ -81,8 +80,7 @@ export default class ProcessPAF extends JBrowseCommand {
         }`
       }
 
-      // eslint-disable-next-line no-console
-      console.log(
+      this.log(
         [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t'),
       )
     }

From d873d7b2421015e0e6d9179610fb46ab62aa6e80 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 4 Dec 2023 12:38:12 -0500
Subject: [PATCH 04/12] Updates

---
 .../PairwiseIndexedPAFAdapter.ts              | 14 ++++----
 .../PairwiseIndexedPAFAdapter/configSchema.ts |  9 ++++--
 products/jbrowse-cli/README.md                | 24 ++++++++++++++
 products/jbrowse-cli/createppaf.sh            |  4 +++
 .../__snapshots__/process-paf.test.ts.snap    | 32 +++++++++----------
 .../jbrowse-cli/src/commands/add-track.ts     | 15 ++++++++-
 .../src/commands/process-paf.test.ts          | 18 ++++++-----
 .../jbrowse-cli/src/commands/process-paf.ts   | 27 +++++++---------
 test_data/hs1_vs_mm39/config.json             | 27 ++++++++--------
 9 files changed, 105 insertions(+), 65 deletions(-)
 create mode 100755 products/jbrowse-cli/createppaf.sh

diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
index 47d97bdcbe..7d2f23262f 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
@@ -22,7 +22,7 @@ interface PAFOptions extends BaseOptions {
 export default class PAFAdapter extends BaseFeatureDataAdapter {
   public static capabilities = ['getFeatures', 'getRefNames']
 
-  protected paf: TabixIndexedFile
+  protected ppaf: TabixIndexedFile
 
   public constructor(
     config: AnyConfigurationModel,
@@ -30,20 +30,20 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const pafGzLoc = this.getConf('pafGzLocation') as FileLocation
+    const ppafGzLoc = this.getConf('ppafGzLocation') as FileLocation
     const type = this.getConf(['index', 'indexType'])
     const loc = this.getConf(['index', 'location'])
     const pm = this.pluginManager
 
-    this.paf = new TabixIndexedFile({
-      filehandle: openLocation(pafGzLoc, pm),
+    this.ppaf = new TabixIndexedFile({
+      filehandle: openLocation(ppafGzLoc, pm),
       csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
       tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
       chunkCacheSize: 50 * 2 ** 20,
     })
   }
   async getHeader() {
-    return this.paf.getHeader()
+    return this.ppaf.getHeader()
   }
 
   getAssemblyNames(): string[] {
@@ -68,7 +68,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     }
 
     const idx = this.getAssemblyNames().indexOf(r1)
-    const names = await this.paf.getReferenceSequenceNames(opts)
+    const names = await this.ppaf.getReferenceSequenceNames(opts)
     if (idx === 0) {
       return names.filter(n => n.startsWith('q')).map(n => n.slice(1))
     } else if (idx === 1) {
@@ -86,7 +86,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
       const flip = index === 0
       const letter = flip ? 't' : 'q'
 
-      await this.paf.getLines(letter + query.refName, query.start, query.end, {
+      await this.ppaf.getLines(letter + query.refName, query.start, query.end, {
         lineCallback: (line, fileOffset) => {
           const r = parsePAFLine(line)
           const refName = r.qname.slice(1)
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
index a585dc67cd..20b6cb9e38 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
@@ -37,10 +37,13 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema(
     /**
      * #slot
      */
-    pafGzLocation: {
+    ppafGzLocation: {
       type: 'fileLocation',
-      description: 'location of pairwise tabix indexed PAF',
-      defaultValue: { uri: '/path/to/data/file.paf.gz' },
+      description: 'location of pairwise tabix indexed PAF (ppaf)',
+      defaultValue: {
+        uri: '/path/to/data/file.ppaf.gz',
+        locationType: 'UriLocation',
+      },
     },
     /**
      * #slot
diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index 6d9edd3654..52e64aad18 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -54,6 +54,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
+- [`jbrowse process-paf TRACK`](#jbrowse-process-paf-track)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -478,6 +479,29 @@ DESCRIPTION
 _See code:
 [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
+## `jbrowse process-paf TRACK`
+
+Pairwise index the PAF
+
+```
+USAGE
+  $ jbrowse process-paf TRACK
+
+ARGUMENTS
+  TRACK  Track file or URL
+
+DESCRIPTION
+  Pairwise index the PAF
+
+EXAMPLES
+  # processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF
+
+  $ jbrowse process-paf file.paf > output.ppaf
+```
+
+_See code:
+[src/commands/process-paf.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/process-paf.ts)_
+
 ## `jbrowse remove-track TRACK`
 
 Remove a track configuration from a JBrowse 2 configuration. Be aware that this
diff --git a/products/jbrowse-cli/createppaf.sh b/products/jbrowse-cli/createppaf.sh
new file mode 100755
index 0000000000..fed4f2765d
--- /dev/null
+++ b/products/jbrowse-cli/createppaf.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+# Usage: createppaf.sh input.paf out.ppaf
+bin/dev process-paf $1 | sort -t$'\t' -k1,1 -k3,3n | bgzip >  $2
+tabix -s1 -b3 -e4 $2
diff --git a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
index 660db3ad5a..5c802aaca1 100644
--- a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
+++ b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
@@ -1,21 +1,19 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`process-paf processes volvox paf 1`] = `15`;
-
-exports[`process-paf processes volvox paf 2`] = `
-"qctgA	49186	26805	49184	+	ctgA	50001	27258	50001	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2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-qctgA	49186	16409	18309	+	ctgA	50001	16650	18559	1708	2080	60	NM:i:372	ms:i:2437	AS:i:2143	nn:i:0	tp:A:P	cm:i:95	s1:i:761	s2:i:212	de:f:0.0792	zd:i:3	rl:i:0	cg:Z:19M5D3M3I13M1D9M1D5M2I5M8D39M1I36M2D33M1D22M1D10M2I8M1D5M1D16M6D5M2D11M2I12M1I7M1I3M3I3M1D3M1I13M1D21M1I4M2I1M1D14M1I12M1I2M1D12M6I5M1D19M10D28M1D26M1D41M1I11M1D9M1I9M4D15M6D13M1D25M5D3M1I27M2D7M1D17M7D18M2I16M1I12M1D22M2I5M12D5M7D2M1D13M1I13M2D2M1I15M1I19M1D17M1I58M1I8M11I8M1I6M2D6M1D2M1I8M2D4M15D6M1D1M2I8M3I25M1D21M1I43M1I6M1D12M2I10M14I5M1D19M3D4M1I95M2D16M2I9M3I8M1I3M1D3M4D1M1D5M3D14M1I7M1I6M2I40M1I1M2I5M1D5M1I11M7D25M10I16M1I2M2D21M1D4M1D4M1D15M2D3M1I13M13I28M2D5M1I33M1I11M1D36M1D19M1I22M1D18M1I1M1I12M1D6M9D11M2D4M1I5M10D16M5I21M1D5M1I11M37I13M3I4M1D9M1I3M1I12M1I58M1D14M
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-qctgA	49186	18309	18754	-	ctgA	50001	18559	19001	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:5M1I15M2I30M1D20M1D13M2D2M1D14M8I11M1D18M1I7M1I56M1D33M1D52M2D7M1I19M7D26M1I9M2I10M1I27M1D18M1I15M2I17M
-qctgA	49186	1860	2214	-	ctgA	50001	1859	2192	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:14M1D4M1D3M1D9M1I12M5D20M2I43M1I10M1I7M2D2M1D8M1I30M1I9M1I2M1I6M15I39M2I16M4I2M1I35M1I2M1I6M1D42M
-tctgA	50001	27258	50001	+	ctgA	49186	26805	49184	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3I58M1D4M1D3M2I20M3D2M1I42M15I1M1I15M6I2M4I24M1I10M1I64M1I62M1D11M2I10M4I23M1D25M4D23M1D20M2I3M1D7M10D7M1D4M1D5M1D15M10D21M1I3M3D6M1I12M1D6M1I30M1D5M1D6M9I4M1I33M1I2M1I8M1I3M1D5M5D25M2D10M1D34M1D6M5I4M4I6M1I34M1I13M1D25M2I19M1D25M1I1M2D24M1D3M1D20M1I2M1D7M1D3M2D6M4D14M2I29M1I3M2I7M1I4M1I6M2I8M4D30M1D8M4I18M1D7M1I3M1I1M1I9M1I11M3I21M5D6M1I1M1I2M1D5M4D27M1D19M1I7M1I9M5D50M1I3M7I33M1I5M1I2M1I32M34I1M1I6M3D40M1I21M2D33M1D2M1D14M1I4M2I17M1D30M1I9M1D53M1I22M1D5M1D6M2I13M4D19M2I6M2D3M1D15M3I4M1D15M1D3M1I8M7D1M1D56M3I12M1I17M1I5M1I52M7I13M1I2M1I4M1D2M3I9M1I18M1D9M6I9M1D1M2I5M1D6M2I3M3I1M2I3M2I17M2I11M5I4M4I12M1I6M1I9M2I3M1D12M1D7M1D17M1D6M1D13M1D15M2D19M2I6M2D2M1D9M2I20M12D12M1I35M3I6M1D23M3I7M1D8M2I7M1D10M1D41M2D20M1I34M1D2M1D10M1D12M2I10M1I13M13I18M1D27M2I13M2D26M3I4M1I9M2D5M3I39M1I19M1I9M1D12M2I33M1I22M1D31M1D28M1I11M2D5M1I22M1I3M27I38M1D8M1I8M1D29M5I8M1D46M1D18M1I6M1I61M1I16M6I4M3I13M1I19M5I4M1I5M2I6M6I4M7I7M1I7M1I7M1D41M5D3M1D11M1I17M1D3M1D3M1D5M1I11M2D30M5D4M1D6M1I18M1I10M1I50M1D8M1D16M1I9M26I11M1D44M1I19M1D9M2I2M1D18M1I8M15D19M1I13M1D8M1D6M1D4M3D7M1I4M1I3M1D2M1D3M3I1M1I20M1D15M1I11M1I22M2D41M2I12M1D7M2I6M8I3M7I2M2I27M1I19M1I2M1I41M1D13M1I38M1I11M4I7M1D14M1I1M3I37M1I2M1I4M1I3M4I2M1I21M1I18M1D11M2I13M1D23M25D15M1D2M1D3M7D18M1D35M1I11M1D5M1D45M4I5M1I7M1I6M1I35M1D34M2D9M1I6M1D47M1D10M1D34M1D5M1I6M1D1M1D4M8D28M3I6M1D19M1I18M1D7M5I5M1I22M1I3M2D5M12I8M1D71M2D23M1D6M1I3M2I5M2D12M1I12M1D24M1I14M1D3M1I24M1I26M22I42M1I9M1D1M1D9M1I6M1I12M1D6M3I17M12I7M1D11M2D19M1I17M1I17M2D2M2D9M2I10M1I6M2I29M1I3M1I19M1D4M3D8M1D1M2D55M1D43M3D42M1D33M22D22M1I3M1I24M1D40M1I21M1I2M1D5M1I2M1I18M1I20M2I12M1D22M1D4M4D84M1D21M1D35M1I3M4I13M1D5M1D10M4D11M1I20M1I5M1I16M1D14M1I8M1D58M1D9M1D5M26D6M1I30M2D7M1D9M1I9M1D38M5D1M2D8M2D14M2I1M2I13M1I2M1D12M1I21M1I8M1I17M2D4M4D7M1D12M1D23M1I12M1D8M8I12M1D5M1I18M1D39M1D2M1I9M1D5M2I16M1I23M3I6M2D17M3I1M1I13M1D49M1I25M1D5M1D13M1D9M1I21M1I6M1D13M1D2M2I3M2I3M1I3M3I22M1D1M1D10M4D1M4D3M2D7M2I3M2D15M1D9M1D3M4I6M7I1M1I16M1D9M1I6M9I4M3I7M1I5M1D7M1I5M1I31M1I10M1D29M1I6M5I4M1D3M5I22M1D1M1D4M4I2M1D15M2D4M1D1M1D5M2I5M2I7M1I6M1I1M1I14M4I25M1I30M1D30M6I15M3D12M1D9M1D72M1D9M1I8M1I6M1D5M1I18M5D3M1I4M3D3M7D17M1I5M1I19M2D3M1D14M3D2M1D10M1D2M1D38M4D2M1I25M1I23M2D4M1D8M1D3M19D16M1I21M1D21M2D6M23D9M1D9M11D3M5D17M1D2M8D5M1D5M1I12M1I25M1I20M1I10M3D2M4I3M1D18M3D6M2I35M1I2M3D2M1I9M1D1M1D14M1I2M10I1M2I4M1D6M5I3M6I1M6I18M1I8M1D6M1D49M1I18M1D1M1D7M2I24M1I13M1I1M26I8M2I2M1D19M1I13M1D9M1D5M1D3M10I10M5D1M1D15M1I27M1D15M1D30M2I12M1I10M3I22M5I4M1I9M1D33M1I3M1I12M9D4M1I6M5D3M8D8M1D33M5D13M1I22M1I12M1D17M6D5M3I12M1D12M1I1M1I7M1D44M1I1M1I12M1D47M1I8M2I27M1I1M1I35M1I9M1D6M3I52M3D6M1D27M1D8M1D13M1I13M4D16M3D43M1D13M1I31M1I63M1I30M1D6M1I1M1I15M20I18M2I15M9I8M3I16M11I9M1I18M1D27M8D2M3D1M1D11M2I24M2I27M1I2M1I52M1D50M1D4M1I7M7I23M1D6M1I34M2D15M2I11M1D9M1I21M6I1M1I11M2D2M1D7M27I18M1D2M1I10M4I12M3I1M2I15M5I1M1I6M6I6M1I40M5D8M1D8M35D6M1D27M1I15M2D3M18D5M4D2M1D4M4D8M1D39M2D5M6I9M38I3M1D24M1I2M1I17M1I9M2I7M9D12M1D1M1D15M1D10M2I11M1I10M1I19M3D20M1I43M1I8M1D4M3D1M2D2M3D5M3I13M1D9M5D6M1I6M1D2M2I23M1D8M1D19M1I12M1D20M1I5M1D16M2D10M15D5M2I7M1D14M4I13M1I16M1D4M1I5M2I5M2I3M1D14M17D6M1D16M6D13M5I1M1I6M1D4M1I2M2D17M1I33M1D4M1I16M1D44M1D19M1D19M1I10M13I13M1D5M2I12M1I4M1D10M1I15M1I5M1D7M1D8M1I30M1I3M1I6M2D30M1I33M2D7M4D8M1I2M1I16M1I20M1D3M1I35M1D5M1I10M4I5M1I3M1I19M2D5M2D8M5D49M1I14M1D15M1D11M1D4M3I5M1I50M1D11M7D2M4D9M1D18M2D11M1D5M2D13M5D3M2I19M2D11M2D47M4D1M2D7M1D26M1I4M1I6M1I6M1D24M2D5M3I9M1I13M1D9M1D22M1I3M1D12M1D4M4I32M1D2M2D15M3I3M1I10M1I7M1I11M1D4M1I3M7D2M1I11M1D4M1D1M2D9M8D15M1D9M1D44M1I4M2I10M1I15M1D23M5D4M2I7M4D14M1I10M2D35M1D5M3I25M1I17M1D18M5I5M2D15M2I21M1I1M1I55M7D11M1I5M1D13M2D13M1D12M1I18M1D9M3D29M1D5M1I11M2D11M1D4M4D13M1I10M3D83M1I24M1I6M2I4M1D5M1I6M1I34M1I4M2I11M1I4M2I47M10D7M1I40M3I11M2D39M1D19M1D2M1D3M1I22M2D17M2D4M1I2M1D7M1D27M1D7M1D17M1D7M1D15M1I8M1D3M1D1M1D44M1D1M3I4M1D2M1D19M1I15M1D6M4I28M1D8M1I13M1D4M1I11M1I19M2D69M1D43M4I24M1I25M2D13M2D16M1I4M1I8M1I42M1D11M1D7M3I1M2I1M5I14M2I2M1D28M1I5M1D25M1I46M7D8M2D30M1D4M1D19M1I22M1D30M1I10M5D7M1D5M1D3M2D12M11I3M1D7M8I2M6I2M3I7M2I4M1D1M2I5M1I18M2D1M1D1M1D4M1D10M3D18M1D27M2I5M1D6M1I7M2D7M22I30M1I31M1I19M2D46M1D3M1D27M6I13M1D37M1D12M2I14M28D3M1D3M1I18M6D25M1D8M1I9M2I17M1I2M4D10M1D44M1D6M1I14M3D10M2I7M1I10M2D9M15D18M1I13M1D15M1I25M1I13M1D1M1D18M5D17M1I16M1I16M1D29M1D24M1I17M1I15M2D10M1D11M3I3M1D2M1I50M11I2M2I2M1I1M2I1M1I9M1I18M2D41M1D26M1D25M1D22M4I6M2I2M13I23M1I11M1I25M1I7M3D9M1D4M1I16M1D4M1I2M1D6M1D20M1I37M2I42M1D3M1I47M1I11M1I3M1I14M1I7M1I19M7I11M3I10M2D7M1D11M1I48M1D2M1D10M4D2M1D18M1I67M2I4M4I6M1I17M1D6M2D23M1I9M1I1M3I8M1I14M2I2M3D6M4I9M1I5M5I22M1I6M2I25M8I1M2I4M1I2M4I31M2D7M1D11M11I16M2I11M2I14M1I8M2I3M1D21M1D6M2D1M1D6M1I27M1I1M1I33M1I21M2I1M1I8M1I5M2I6M1I8M1D34M1I3M4D7M1D2M1D16M1D1M1D46M1I12M1D7M1D31M6D10M1D1M1D1M1D5M11D10M1D19M1I22M1I10M1I11M1D8M1D24M1I6M2D7M3I2M1I17M1D24M1D2M4I19M1D14M2I17M1I9M3D16M1I10M1I25M1D26M11I3M2I5M1I2M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-tctgA	50001	16650	18559	+	ctgA	49186	16409	18309	1708	2080	60	NM:i:372	ms:i:2437	AS:i:2143	nn:i:0	tp:A:P	cm:i:95	s1:i:761	s2:i:212	de:f:0.0792	zd:i:3	rl:i:0	cg:Z:19M5I3M3D13M1I9M1I5M2D5M8I39M1D36M2I33M1I22M1I10M2D8M1I5M1I16M6I5M2I11M2D12M1D7M1D3M3D3M1I3M1D13M1I21M1D4M2D1M1I14M1D12M1D2M1I12M6D5M1I19M10I28M1I26M1I41M1D11M1I9M1D9M4I15M6I13M1I25M5I3M1D27M2I7M1I17M7I18M2D16M1D12M1I22M2D5M12I5M7I2M1I13M1D13M2I2M1D15M1D19M1I17M1D58M1D8M11D8M1D6M2I6M1I2M1D8M2I4M15I6M1I1M2D8M3D25M1I21M1D43M1D6M1I12M2D10M14D5M1I19M3I4M1D95M2I16M2D9M3D8M1D3M1I3M4I1M1I5M3I14M1D7M1D6M2D40M1D1M2D5M1I5M1D11M7I25M10D16M1D2M2I21M1I4M1I4M1I15M2I3M1D13M13D28M2I5M1D33M1D11M1I36M1I19M1D22M1I18M1D1M1D12M1I6M9I11M2I4M1D5M10I16M5D21M1I5M1D11M37D13M3D4M1I9M1D3M1D12M1D58M1I14M
-tctgA	50001	0	1859	+	ctgA	49186	3	1851	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1D16M1D5M3D33M1I14M3I7M1I25M2D5M2D4M1I17M3I11M1I5M3I3M1D15M3D1M2D6M1D2M6I6M2I24M1D3M2I29M1D2M1D3M1D6M1D10M2I8M19I33M1I23M2I9M1I11M1D6M1I5M1I28M1D13M1I5M1D2M1D49M5I6M2D21M1I1M2I2M2I4M4D4M1D5M1D3M1I2M1D4M37I17M2D16M6I5M3I3M6I16M5D4M8D5M4D1M1D52M2I2M1D5M28I33M1I17M2D2M2I31M42D5M1D9M1D7M1I8M1D40M1D39M1D2M1I3M2D11M2D6M2D10M1I14M1D12M1D16M1I6M3D6M2D4M1D1M1D27M1D3M10D3M2I11M3I3M1D35M1D1M3I3M2I19M3I9M4I23M1D3M1D28M1D52M1D28M1I20M2D66M1D3M2D7M1I7M2I9M1I11M1I11M1I7M1D3M1D30M1I11M1I15M2D7M3I3M1D12M6D35M1I4M1I17M1I15M1D5M1I4M1D5M1D3M5I10M1I2M1I8M7D13M5D9M1I4M1D45M6D4M1D19M2I16M1I1M2D23M7D11M1D19M1I13M
-tctgA	50001	18559	19001	-	ctgA	49186	18309	18754	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:17M2D15M1D18M1I27M1D10M2D9M1D26M7I19M1D7M2I52M1I33M1I56M1D7M1D18M1I11M8D14M1I2M2I13M1I20M1I30M2D15M1D5M
-tctgA	50001	1859	2192	-	ctgA	49186	1860	2214	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
+exports[`process-paf processes volvox paf 1`] = `
+"tctgA	49186	26805	49184	+	ctgA	50001	27258	50001	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2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+qctgA	50001	1859	2192	-	ctgA	49186	1860	2214	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
 "
 `;
diff --git a/products/jbrowse-cli/src/commands/add-track.ts b/products/jbrowse-cli/src/commands/add-track.ts
index 0dc2031f4c..27a5ccbd86 100644
--- a/products/jbrowse-cli/src/commands/add-track.ts
+++ b/products/jbrowse-cli/src/commands/add-track.ts
@@ -268,6 +268,7 @@ export default class AddTrack extends JBrowseCommand {
     if (
       [
         'PAFAdapter',
+        'PairwiseIndexedPAFAdapter',
         'DeltaAdapter',
         'ChainAdapter',
         'MashMapAdapter',
@@ -276,6 +277,7 @@ export default class AddTrack extends JBrowseCommand {
       ].includes(adapter.type)
     ) {
       // @ts-expect-error
+      // this is for the adapter's assembly names
       adapter.assemblyNames = assemblyNames.split(',').map(a => a.trim())
     }
 
@@ -425,7 +427,8 @@ export default class AddTrack extends JBrowseCommand {
     } else if (
       /\.gff3?\.b?gz$/i.test(location) ||
       /\.vcf\.b?gz$/i.test(location) ||
-      /\.bed\.b?gz$/i.test(location)
+      /\.bed\.b?gz$/i.test(location) ||
+      /\.ppaf\.b?gz$/i.test(location)
     ) {
       return {
         file: location,
@@ -543,6 +546,15 @@ export default class AddTrack extends JBrowseCommand {
         type: 'BedAdapter',
         bedLocation: makeLocation(location),
       }
+    } else if (/\.ppaf\.b?gz$/i.test(location)) {
+      return {
+        type: 'PairwiseIndexedPAFAdapter',
+        ppafGzLocation: makeLocation(location),
+        index: {
+          location: makeLocation(index || `${location}.tbi`),
+          indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
+        },
+      }
     } else if (/\.bed\.b?gz$/i.test(location)) {
       return {
         type: 'BedTabixAdapter',
@@ -657,6 +669,7 @@ export default class AddTrack extends JBrowseCommand {
       DeltaAdapter: 'SyntenyTrack',
       ChainAdapter: 'SyntenyTrack',
       MashMapAdapter: 'SyntenyTrack',
+      PairwiseIndexedPAFAdapter: 'SyntenyTrack',
       MCScanAnchorsAdapter: 'SyntenyTrack',
       MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
     }
diff --git a/products/jbrowse-cli/src/commands/process-paf.test.ts b/products/jbrowse-cli/src/commands/process-paf.test.ts
index dac2e56686..7c6ab47434 100644
--- a/products/jbrowse-cli/src/commands/process-paf.test.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.test.ts
@@ -10,12 +10,14 @@ const base = path.join(__dirname, '..', '..', 'test', 'data')
 const simplePaf = path.join(base, 'volvox_inv_indels.paf')
 
 describe('process-paf', () => {
-  setup.command(['process-paf', simplePaf]).it('processes volvox paf', ctx => {
-    let res = ''
-    for (const obj of ctx.stdoutWrite.mock.calls) {
-      res += obj[0]
-    }
-    expect(res.split('\n').length).toMatchSnapshot()
-    expect(res).toMatchSnapshot()
-  })
+  setup
+    .command(['process-paf', simplePaf])
+    .it('processes volvox paf', async ctx => {
+      let res = ''
+      for (const obj of ctx.stdout) {
+        res += obj[0]
+      }
+      expect(res.split('\n').length).toBe(15)
+      expect(res).toMatchSnapshot()
+    })
 })
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/process-paf.ts
index 154011a82f..0d8cef380e 100644
--- a/products/jbrowse-cli/src/commands/process-paf.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.ts
@@ -3,6 +3,7 @@ import JBrowseCommand from '../base'
 
 import readline from 'readline'
 import { createGunzip } from 'zlib'
+import { Args } from '@oclif/core'
 
 function getReadline(filename: string) {
   const stream = fs.createReadStream(filename)
@@ -47,27 +48,20 @@ export default class ProcessPAF extends JBrowseCommand {
     '$ jbrowse process-paf file.paf > output.ppaf',
   ]
 
-  static args = [
-    {
-      name: 'track',
+  static args = {
+    track: Args.string({
       required: true,
       description: `Track file or URL`,
-    },
-  ]
+    }),
+  }
 
   async run() {
-    const { args: runArgs } = this.parse(ProcessPAF)
-
+    const { args: runArgs } = await this.parse(ProcessPAF)
     const { track: filename } = runArgs
 
     const rl1 = getReadline(filename)
     for await (const line of rl1) {
-      this.log(`q${line}`)
-    }
-    rl1.close()
-
-    const rl2 = getReadline(filename)
-    for await (const line of rl2) {
+      process.stdout.write(`t${line}\n`)
       const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
       const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
 
@@ -80,10 +74,11 @@ export default class ProcessPAF extends JBrowseCommand {
         }`
       }
 
-      this.log(
-        [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t'),
+      process.stdout.write(
+        [`q${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') +
+          '\n',
       )
     }
-    rl2.close()
+    rl1.close()
   }
 }
diff --git a/test_data/hs1_vs_mm39/config.json b/test_data/hs1_vs_mm39/config.json
index 8b31c9381c..15b8e1ff2b 100644
--- a/test_data/hs1_vs_mm39/config.json
+++ b/test_data/hs1_vs_mm39/config.json
@@ -76,10 +76,10 @@
         }
       }
     },
-
     {
       "type": "FeatureTrack",
       "trackId": "ncbiRefSeq",
+      "category": ["Annotation"],
       "name": "ncbiRefSeq",
       "adapter": {
         "type": "BigBedAdapter",
@@ -92,8 +92,8 @@
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "liftover",
-      "name": "liftover",
+      "trackId": "hs1ToMm39.over.chain",
+      "name": "hs1ToMm39.over.chain",
       "adapter": {
         "type": "ChainAdapter",
         "chainLocation": {
@@ -107,23 +107,24 @@
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "liftover_pairwise_paf",
-      "name": "liftover_pairwise_paf",
+      "trackId": "hs1ToMm39.over.chain.ppaf",
+      "name": "hs1ToMm39.over.chain.ppaf",
       "adapter": {
         "type": "PairwiseIndexedPAFAdapter",
-        "pafGzLocation": {
-          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1_vs_mm39.paf.gz"
+        "ppafGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1ToMm39.over.chain.ppaf.gz",
+          "locationType": "UriLocation"
         },
         "index": {
           "location": {
-            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1_vs_mm39.paf.gz.tbi"
-          }
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1ToMm39.over.chain.ppaf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
         },
-
-        "targetAssembly": "hs1",
-        "queryAssembly": "mm39"
+        "assemblyNames": ["mm39", "hs1"]
       },
-      "assemblyNames": ["hs1", "mm39"]
+      "assemblyNames": ["mm39", "hs1"]
     }
   ]
 }

From 3795f733472dfa1c267ef119e758a46825b564e5 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 4 Dec 2023 20:45:42 -0500
Subject: [PATCH 05/12] Misc

---
 plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts | 6 +++++-
 .../PairwiseIndexedPAFAdapter.ts                          | 2 +-
 products/jbrowse-cli/src/commands/process-paf.ts          | 8 ++++++--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
index ee76e3462a..f87863e5c8 100644
--- a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts
@@ -104,6 +104,9 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
       // adapter in the subadapters list
       const { start: qstart, end: qend, refName: qref, assemblyName } = query
       const index = assemblyNames.indexOf(assemblyName)
+
+      // if the getFeatures::query is on the query assembly, flip orientation
+      // of data
       const flip = index === 0
       if (index === -1) {
         console.warn(`${assemblyName} not found in this adapter`)
@@ -118,7 +121,8 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
         let mateName = ''
         let mateStart = 0
         let mateEnd = 0
-        if (index === 0) {
+
+        if (flip) {
           start = r.qstart
           end = r.qend
           refName = r.qname
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
index 7d2f23262f..90ec462bbd 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
@@ -84,7 +84,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
       const assemblyNames = this.getAssemblyNames()
       const index = assemblyNames.indexOf(assemblyName)
       const flip = index === 0
-      const letter = flip ? 't' : 'q'
+      const letter = flip ? 'q' : 't'
 
       await this.ppaf.getLines(letter + query.refName, query.start, query.end, {
         lineCallback: (line, fileOffset) => {
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/process-paf.ts
index 0d8cef380e..a059885301 100644
--- a/products/jbrowse-cli/src/commands/process-paf.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.ts
@@ -61,8 +61,12 @@ export default class ProcessPAF extends JBrowseCommand {
 
     const rl1 = getReadline(filename)
     for await (const line of rl1) {
-      process.stdout.write(`t${line}\n`)
       const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
+
+      process.stdout.write(
+        [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') +
+          '\n',
+      )
       const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
 
       const CIGAR = rest[cigarIdx]
@@ -75,7 +79,7 @@ export default class ProcessPAF extends JBrowseCommand {
       }
 
       process.stdout.write(
-        [`q${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') +
+        [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') +
           '\n',
       )
     }

From d28d55ebc5800e7dbfddb1b6922176230d917a2a Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 4 Dec 2023 20:53:19 -0500
Subject: [PATCH 06/12] Mis

---
 products/jbrowse-cli/README.md                | 36 +++++++++++++++----
 .../__snapshots__/process-paf.test.ts.snap    | 28 +++++++--------
 .../jbrowse-cli/src/commands/process-paf.ts   | 31 +++++++++++-----
 products/jbrowse-cli/src/commands/sort-gff.ts |  6 +++-
 4 files changed, 72 insertions(+), 29 deletions(-)

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index 52e64aad18..a94f22cc53 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -54,7 +54,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
-- [`jbrowse process-paf TRACK`](#jbrowse-process-paf-track)
+- [`jbrowse process-paf [TRACK]`](#jbrowse-process-paf-track)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -479,16 +479,19 @@ DESCRIPTION
 _See code:
 [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
-## `jbrowse process-paf TRACK`
+## `jbrowse process-paf [TRACK]`
 
 Pairwise index the PAF
 
 ```
 USAGE
-  $ jbrowse process-paf TRACK
+  $ jbrowse process-paf [TRACK] [-h]
 
 ARGUMENTS
-  TRACK  Track file or URL
+  TRACK  Track file or URL (optional, stdin if not specified)
+
+FLAGS
+  -h, --help  Show CLI help.
 
 DESCRIPTION
   Pairwise index the PAF
@@ -496,7 +499,25 @@ DESCRIPTION
 EXAMPLES
   # processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF
 
-  $ jbrowse process-paf file.paf > output.ppaf
+
+
+  # read from stdin. could also pipe directly from minimap2 here
+
+  $ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.ppaf.gz
+
+  $ tabix out.ppaf.gz
+
+  $ jbrowse add-track out.ppaf.gz -a mm39,hg38
+
+
+
+  # read from file instead of stdin
+
+  $ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.ppaf.gz
+
+  $ tabix out.ppaf.gz
+
+  $ jbrowse add-track out.ppaf.gz -a mm39,hg38
 ```
 
 _See code:
@@ -577,11 +598,14 @@ sort and grep
 
 ```
 USAGE
-  $ jbrowse sort-gff FILE
+  $ jbrowse sort-gff FILE [-h]
 
 ARGUMENTS
   FILE  GFF file
 
+FLAGS
+  -h, --help  Show CLI help.
+
 DESCRIPTION
   Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
   refname and start position using unix utilities sort and grep
diff --git a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
index 5c802aaca1..610243d7a6 100644
--- a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
+++ b/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
@@ -1,19 +1,19 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`process-paf processes volvox paf 1`] = `
-"tctgA	49186	26805	49184	+	ctgA	50001	27258	50001	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2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-qctgA	50001	19011	26774	+	ctgA	49186	18755	26306	6872	8319	60	NM:i:1447	ms:i:9750	AS:i:8692	nn:i:0	tp:A:P	cm:i:376	s1:i:3010	s2:i:212	de:f:0.0832	zd:i:3	rl:i:0	cg:Z:17M1D43M1I4M7I2M7I13M2D3M1D7M1D19M1I5M1I32M1I5M2D63M4I20M5I50M2D12M1D16M3I8M1D19M2I38M1I28M7D2M1D5M4D1M1D3M2D2M1I25M1D10M1I2M1I19M1D5M1I32M1D8M5I4M8I7M1I1M1I26M2I16M2D6M7I14M4D2M1D3M2D4M1I32M6D8M1I12M1I10M1I24M4I2M1I43M1I22M1D11M1D30M2I31M1I19M1I2M1I10M3D48M1D26M4I11M1I4M1I11M2I4M1I18M7D8M1D10M1D2M1I61M1I4M1D18M1I13M3I3M2I5M8I47M1D30M3I6M1D44M2I14M1D40M9I1M2I24M1I16M39D5M1D38M3D22M4I35M1D19M1D19M1D26M1I4M1D10M4I39M1D10M2D10M1D10M1D3M1I1M5I16M1D13M1I11M1I25M1I21M8D22M4I11M1I9M5I17M1I73M1D36M6I4M1I19M1D52M1D15M24D1M1D2M2D15M1D2M6D2M1D28M1I41M4D46M4D14M1I7M21I4M1D20M1I2M1D15M1D3M1D29M1D20M5I37M2D9M1D16M1D24M1D22M3I1M2I47M1D6M1I6M1D19M1I18M1D1M1D18M1D3M1D2M1D5M35I8M1I13M1D7M4D31M1D6M1I83M2I1M1D26M1D15M1D3M2I5M2I12M1I42M1D1M2D12M4I2M4I6M26I8M3I1M1I2M4I9M1I30M2I3M2I28M1D4M1D41M1I18M1D41M1D12M1D19M4D35M5D31M4D31M1D3M1I11M1D25M2I2M3I30M1I5M1D8M1I22M1D7M1I32M1D29M6I1M7I10M3I1M1I5M1D15M7D18M2D10M4I42M1I15M1D13M1I5M1I2M2D38M1D9M2D7M3D20M1I15M1D5M1I3M1I8M2D12M1I10M1I3M1I6M1I30M1I94M1D18M1D4M5I3M1I29M1I2M1I2M1I5M1D4M1I13M1D9M6D10M1I6M1I12M2D5M2I1M1I11M2I1M1I10M5I9M8I17M1I35M1I4M1D16M5D1M1D9M8D21M23D2M1D38M1I1M1I8M1I27M1D42M1D9M2I1M1D5M1I23M2D5M1D28M1I25M1I24M1I5M1D21M1D4M4D7M1I7M1D25M21D5M1D4M1D42M2I26M1I7M1D10M1D1M1D19M10I4M1I14M1I42M8I28M3I2M3I13M1D17M1I11M1D22M1D19M1D1M4D9M2I2M1D14M8D9M2I9M1D13M2I11M3I2M2D5M1D3M1D6M3I10M1D9M1I21M1D5M2D9M2D10M1I3M2D9M1D21M3I23M1D8M1D3M1D26M1D33M8I7M1D9M10I10M1D7M1I52M10I13M1D6M2I39M1I6M1I26M1D4M1I4M32I24M1I21M2I1M1I7M1I1M1I15M1I5M1I24M2D1M1D6M1I2M1I19M35I41M3D6M3D15M2I3M1I14M2D9M3I19M2I26M1I30M1D6M3I32M1D5M1I36M1I8M1I2M2I2M1I6M3D3M7D2M2D17M1I12M1I6M1D40M3I28M2D2M2D21M1I4M1D9M1D4M1D31M2D11M1I31M1I3M2I3M5I7M4I7M1I6M1I6M8I4M1D1M2I19M3D14M1I7M1I12M1D4M3D2M4D11M1D8M1D17M1I11M1I3M1I15M17D8M3I42M1D17M1I25M1D15M1D11M2D7M1I23M4D14M2I20M1D9M3I2M1I17M1I34M1D3M1D4M1I13M1D2M1D6M1D6M1I12M2I1M4I2M4I4M1D16M36I6M1I32M1I27M1I4M1I2M1D11M20I16M3I4M1D16M1I27M1I14M1I21M2D14M1I10M3I5M2I3M3I2M1I1M4I5M1I2M3I7M1I7M1D9M1I5M1I4M1I16M1I9M9I1M1I2M1I4M1I3M2D6M2I5M1D22M1I3M1D8M1I8M3I43M1D4M1I31M1D17M3D8M2D12M6D13M1D16M1I11M2I4M1D5M2I2M2I2M1D29M1D12M2I13M1D7M14I1M1I3M5I10M1I12M5D19M1D10M1D3M7D2M14D3M9D13M2D5M1D13M1I4M1I18M1D3M1I28M1D5M4I35M1I23M3I11M2D8M1I17M1D9M1D23M4I4M1I9M1D3M1D26M1D5M3D1M1D14M1I42M1D5M16D15M1I28M4I5M1D5M1I4M1I11M2I5M1D4M1D3M1D9M
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-qctgA	50001	0	1859	+	ctgA	49186	3	1851	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1D16M1D5M3D33M1I14M3I7M1I25M2D5M2D4M1I17M3I11M1I5M3I3M1D15M3D1M2D6M1D2M6I6M2I24M1D3M2I29M1D2M1D3M1D6M1D10M2I8M19I33M1I23M2I9M1I11M1D6M1I5M1I28M1D13M1I5M1D2M1D49M5I6M2D21M1I1M2I2M2I4M4D4M1D5M1D3M1I2M1D4M37I17M2D16M6I5M3I3M6I16M5D4M8D5M4D1M1D52M2I2M1D5M28I33M1I17M2D2M2I31M42D5M1D9M1D7M1I8M1D40M1D39M1D2M1I3M2D11M2D6M2D10M1I14M1D12M1D16M1I6M3D6M2D4M1D1M1D27M1D3M10D3M2I11M3I3M1D35M1D1M3I3M2I19M3I9M4I23M1D3M1D28M1D52M1D28M1I20M2D66M1D3M2D7M1I7M2I9M1I11M1I11M1I7M1D3M1D30M1I11M1I15M2D7M3I3M1D12M6D35M1I4M1I17M1I15M1D5M1I4M1D5M1D3M5I10M1I2M1I8M7D13M5D9M1I4M1D45M6D4M1D19M2I16M1I1M2D23M7D11M1D19M1I13M
-tctgA	49186	18309	18754	-	ctgA	50001	18559	19001	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:5M1I15M2I30M1D20M1D13M2D2M1D14M8I11M1D18M1I7M1I56M1D33M1D52M2D7M1I19M7D26M1I9M2I10M1I27M1D18M1I15M2I17M
-qctgA	50001	18559	19001	-	ctgA	49186	18309	18754	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:17M2D15M1D18M1I27M1D10M2D9M1D26M7I19M1D7M2I52M1I33M1I56M1D7M1D18M1I11M8D14M1I2M2I13M1I20M1I30M2D15M1D5M
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-qctgA	50001	1859	2192	-	ctgA	49186	1860	2214	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
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 "
 `;
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/process-paf.ts
index a059885301..49c9581921 100644
--- a/products/jbrowse-cli/src/commands/process-paf.ts
+++ b/products/jbrowse-cli/src/commands/process-paf.ts
@@ -3,7 +3,7 @@ import JBrowseCommand from '../base'
 
 import readline from 'readline'
 import { createGunzip } from 'zlib'
-import { Args } from '@oclif/core'
+import { Args, Flags } from '@oclif/core'
 
 function getReadline(filename: string) {
   const stream = fs.createReadStream(filename)
@@ -12,6 +12,12 @@ function getReadline(filename: string) {
   })
 }
 
+function getStdReadline() {
+  return readline.createInterface({
+    input: process.stdin,
+  })
+}
+
 const cigarRegex = new RegExp(/([MIDNSHPX=])/)
 
 export function parseCigar(cigar = '') {
@@ -38,28 +44,37 @@ export function swapIndelCigar(cigar: string) {
 }
 
 export default class ProcessPAF extends JBrowseCommand {
-  // @ts-expect-error
-  target: string
-
   static description = 'Pairwise index the PAF'
 
   static examples = [
     '# processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF',
-    '$ jbrowse process-paf file.paf > output.ppaf',
+    '',
+    '# read from stdin. could also pipe directly from minimap2 here',
+    '$ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.ppaf.gz',
+    '$ tabix out.ppaf.gz',
+    '$ jbrowse add-track out.ppaf.gz -a mm39,hg38',
+    '',
+    '# read from file instead of stdin',
+    '$ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.ppaf.gz',
+    '$ tabix out.ppaf.gz',
+    '$ jbrowse add-track out.ppaf.gz -a mm39,hg38',
   ]
 
   static args = {
     track: Args.string({
-      required: true,
-      description: `Track file or URL`,
+      description: `Track file or URL (optional, stdin if not specified)`,
     }),
   }
 
+  static flags = {
+    help: Flags.help({ char: 'h' }),
+  }
+
   async run() {
     const { args: runArgs } = await this.parse(ProcessPAF)
     const { track: filename } = runArgs
 
-    const rl1 = getReadline(filename)
+    const rl1 = filename ? getReadline(filename) : getStdReadline()
     for await (const line of rl1) {
       const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
 
diff --git a/products/jbrowse-cli/src/commands/sort-gff.ts b/products/jbrowse-cli/src/commands/sort-gff.ts
index 34746a7d3f..15a5c0a8c3 100644
--- a/products/jbrowse-cli/src/commands/sort-gff.ts
+++ b/products/jbrowse-cli/src/commands/sort-gff.ts
@@ -1,4 +1,4 @@
-import { Args } from '@oclif/core'
+import { Args, Flags } from '@oclif/core'
 import { sync as commandExistsSync } from 'command-exists'
 
 import { spawn } from 'child_process'
@@ -21,6 +21,10 @@ export default class SortGff extends JBrowseCommand {
     }),
   }
 
+  static flags = {
+    help: Flags.help({ char: 'h' }),
+  }
+
   async run() {
     const {
       args: { file },

From 5bd7de7dd25a2cc0c98b4471092e8e8baf9c80d1 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 08:39:01 -0500
Subject: [PATCH 07/12] Rename ppaf->pif, rename process-paf to create-pif, add
 new create-pifgz

---
 .gitignore                                    |  1 +
 .../PairwiseIndexedPAFAdapter.ts              | 14 +--
 .../PairwiseIndexedPAFAdapter/configSchema.ts |  6 +-
 products/jbrowse-cli/README.md                | 85 +++++++++++++------
 products/jbrowse-cli/createppaf.sh            |  4 -
 ...f.test.ts.snap => create-pif.test.ts.snap} |  2 +-
 .../jbrowse-cli/src/commands/add-track.ts     |  6 +-
 ...process-paf.test.ts => create-pif.test.ts} |  4 +-
 .../{process-paf.ts => create-pif.ts}         | 22 ++---
 .../src/commands/create-pifgz.test.ts         | 20 +++++
 .../jbrowse-cli/src/commands/create-pifgz.ts  | 64 ++++++++++++++
 test_data/hs1_vs_mm39/config.json             |  6 +-
 12 files changed, 174 insertions(+), 60 deletions(-)
 delete mode 100755 products/jbrowse-cli/createppaf.sh
 rename products/jbrowse-cli/src/commands/__snapshots__/{process-paf.test.ts.snap => create-pif.test.ts.snap} (99%)
 rename products/jbrowse-cli/src/commands/{process-paf.test.ts => create-pif.test.ts} (86%)
 rename products/jbrowse-cli/src/commands/{process-paf.ts => create-pif.ts} (81%)
 create mode 100644 products/jbrowse-cli/src/commands/create-pifgz.test.ts
 create mode 100644 products/jbrowse-cli/src/commands/create-pifgz.ts

diff --git a/.gitignore b/.gitignore
index 5a3a883bc7..7322edaaad 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,3 +19,4 @@ lerna-debug.log
 .yarn
 .yarnrc
 *.tsbuildinfo
+products/jbrowse-cli/test/data/volvox_inv_indels.paf.pif.gz*
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
index 90ec462bbd..8ccc4ecc66 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
@@ -22,7 +22,7 @@ interface PAFOptions extends BaseOptions {
 export default class PAFAdapter extends BaseFeatureDataAdapter {
   public static capabilities = ['getFeatures', 'getRefNames']
 
-  protected ppaf: TabixIndexedFile
+  protected pif: TabixIndexedFile
 
   public constructor(
     config: AnyConfigurationModel,
@@ -30,20 +30,20 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const ppafGzLoc = this.getConf('ppafGzLocation') as FileLocation
+    const pifGzLoc = this.getConf('pifGzLocation') as FileLocation
     const type = this.getConf(['index', 'indexType'])
     const loc = this.getConf(['index', 'location'])
     const pm = this.pluginManager
 
-    this.ppaf = new TabixIndexedFile({
-      filehandle: openLocation(ppafGzLoc, pm),
+    this.pif = new TabixIndexedFile({
+      filehandle: openLocation(pifGzLoc, pm),
       csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
       tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
       chunkCacheSize: 50 * 2 ** 20,
     })
   }
   async getHeader() {
-    return this.ppaf.getHeader()
+    return this.pif.getHeader()
   }
 
   getAssemblyNames(): string[] {
@@ -68,7 +68,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     }
 
     const idx = this.getAssemblyNames().indexOf(r1)
-    const names = await this.ppaf.getReferenceSequenceNames(opts)
+    const names = await this.pif.getReferenceSequenceNames(opts)
     if (idx === 0) {
       return names.filter(n => n.startsWith('q')).map(n => n.slice(1))
     } else if (idx === 1) {
@@ -86,7 +86,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
       const flip = index === 0
       const letter = flip ? 'q' : 't'
 
-      await this.ppaf.getLines(letter + query.refName, query.start, query.end, {
+      await this.pif.getLines(letter + query.refName, query.start, query.end, {
         lineCallback: (line, fileOffset) => {
           const r = parsePAFLine(line)
           const refName = r.qname.slice(1)
diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
index 20b6cb9e38..6c9009291d 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts
@@ -37,11 +37,11 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema(
     /**
      * #slot
      */
-    ppafGzLocation: {
+    pifGzLocation: {
       type: 'fileLocation',
-      description: 'location of pairwise tabix indexed PAF (ppaf)',
+      description: 'location of pairwise tabix indexed PAF (pif)',
       defaultValue: {
-        uri: '/path/to/data/file.ppaf.gz',
+        uri: '/path/to/data/file.pif.gz',
         locationType: 'UriLocation',
       },
     },
diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index a94f22cc53..0f88a79d58 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -53,8 +53,9 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track)
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
+- [`jbrowse create-pif [TRACK]`](#jbrowse-create-pif-track)
+- [`jbrowse create-pifgz FILE [OUTPUT]`](#jbrowse-create-pifgz-file-output)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
-- [`jbrowse process-paf [TRACK]`](#jbrowse-process-paf-track)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -458,70 +459,102 @@ EXAMPLES
 _See code:
 [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse help [COMMANDS]`
+## `jbrowse create-pif [TRACK]`
 
-Display help for jbrowse.
+Create pairwise indexed PAF file (PIF)
 
 ```
 USAGE
-  $ jbrowse help [COMMANDS] [-n]
+  $ jbrowse create-pif [TRACK] [-h]
 
 ARGUMENTS
-  COMMANDS  Command to show help for.
+  TRACK  Track file (optional, reads from stdin if not specified)
 
 FLAGS
-  -n, --nested-commands  Include all nested commands in the output.
+  -h, --help  Show CLI help.
 
 DESCRIPTION
-  Display help for jbrowse.
+  Create pairwise indexed PAF file (PIF)
+
+EXAMPLES
+  # processes a local PAF file into our custom format, PIF (pairwise indexed PAF)
+
+
+
+  # read from stdin. could also pipe directly from minimap2 here
+
+  $ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.pif.gz
+
+  $ tabix out.pif.gz
+
+  $ jbrowse add-track out.pif.gz -a mm39,hg38
+
+
+
+  # read from file instead of stdin
+
+  $ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.pif.gz
+
+  $ tabix out.pif.gz
+
+  $ jbrowse add-track out.pif.gz -a mm39,hg38
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
+[src/commands/create-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pif.ts)_
 
-## `jbrowse process-paf [TRACK]`
+## `jbrowse create-pifgz FILE [OUTPUT]`
 
-Pairwise index the PAF
+Helper utility to sort GFF files for tabix. Moves all lines starting with # to
+the top of the file, and sort by refname and start position using unix utilities
+sort and grep
 
 ```
 USAGE
-  $ jbrowse process-paf [TRACK] [-h]
+  $ jbrowse create-pifgz FILE [OUTPUT] [-h]
 
 ARGUMENTS
-  TRACK  Track file or URL (optional, stdin if not specified)
+  FILE    GFF file
+  OUTPUT  Where to write the output file. If unspecified, will be ${file}.pif.gz
 
 FLAGS
   -h, --help  Show CLI help.
 
 DESCRIPTION
-  Pairwise index the PAF
+  Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
+  refname and start position using unix utilities sort and grep
 
 EXAMPLES
-  # processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF
-
-
-
-  # read from stdin. could also pipe directly from minimap2 here
+  # sort gff and pipe to bgzip
 
-  $ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.ppaf.gz
+  $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
 
-  $ tabix out.ppaf.gz
+  $ tabix sorted.gff.gz
+```
 
-  $ jbrowse add-track out.ppaf.gz -a mm39,hg38
+_See code:
+[src/commands/create-pifgz.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pifgz.ts)_
 
+## `jbrowse help [COMMANDS]`
 
+Display help for jbrowse.
 
-  # read from file instead of stdin
+```
+USAGE
+  $ jbrowse help [COMMANDS] [-n]
 
-  $ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.ppaf.gz
+ARGUMENTS
+  COMMANDS  Command to show help for.
 
-  $ tabix out.ppaf.gz
+FLAGS
+  -n, --nested-commands  Include all nested commands in the output.
 
-  $ jbrowse add-track out.ppaf.gz -a mm39,hg38
+DESCRIPTION
+  Display help for jbrowse.
 ```
 
 _See code:
-[src/commands/process-paf.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/process-paf.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
 ## `jbrowse remove-track TRACK`
 
diff --git a/products/jbrowse-cli/createppaf.sh b/products/jbrowse-cli/createppaf.sh
deleted file mode 100755
index fed4f2765d..0000000000
--- a/products/jbrowse-cli/createppaf.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-# Usage: createppaf.sh input.paf out.ppaf
-bin/dev process-paf $1 | sort -t$'\t' -k1,1 -k3,3n | bgzip >  $2
-tabix -s1 -b3 -e4 $2
diff --git a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
similarity index 99%
rename from products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
rename to products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
index 610243d7a6..bb837cbf18 100644
--- a/products/jbrowse-cli/src/commands/__snapshots__/process-paf.test.ts.snap
+++ b/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`process-paf processes volvox paf 1`] = `
+exports[`create-pif processes volvox paf 1`] = `
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 tctgA	50001	2212	16198	+	ctgA	49186	2214	15925	12504	15030	60	NM:i:2526	ms:i:17647	AS:i:15934	nn:i:0	tp:A:P	cm:i:637	s1:i:5099	s2:i:212	de:f:0.0837	zd:i:3	rl:i:0	cg:Z:10M1I4M2I21M1I10M1I14M1I5M1D29M2D9M1I15M1I27M1I12M1D5M1I11M1D7M2I4M2D9M1D4M6D32M1D13M1I55M1I8M1I1M1I12M1I2M1D22M2I56M1D11M1I5M5I17M3I3M1I13M1D16M1I50M1I2M1I10M1D1M1D42M1D2M2D33M22I3M1I2M1I6M1D8M2D5M1D50M1D6M3D6M2D12M3I13M1D9M5D1M1D10M1I3M1D5M1I3M1I4M1I24M1I5M2D30M1D3M1I15M1D9M1I3M1I18M1I9M1D11M2D6M1I23M4D1M1D22M1I3M1I11M2D1M1D7M1D4M1D18M1I6M1I5M2D5M1I66M2I3M1D8M1I13M1I8M1I3M2D4M1D20M1I5M2I22M1I6M8I14M1I6M1D8M2D5M9D7M2I4M1D11M1I20M2D2M1I33M8I10M2I7M1I18M4I5M1D4M4D1M1D33M3I10M1D20M2D8M1D9M1I10M1D7M1I8M1D6M2I66M1I3M2I2M1I24M1D63M1I14M8I7M1I13M1D31M1I16M4D41M1D3M1D4M23I9M1D2M1D8M1I1M1I12M1I2M1I3M1D33M1I24M2I3M1I4M1I12M122D6M4D2M1D13M1I3M1D35M1I4M1I13M1D32M1D6M1I5M1I5M1D12M1D8M1D48M1I2M1D19M1D9M1I24M1D13M1D8M1I5M7I5M2D10M1I11M3I15M1I6M2I4M1I18M1D14M1D3M1D1M2D17M1D12M4D15M1I3M1D31M1D1M1D1M1D1M1D12M5I2M1D31M2I18M1D5M20D10M1I20M3D11M1I14M1I1M9I4M4I2M4I2M3I4M1D10M1D50M1I14M1I11M8I11M2D9M1I20M3I5M1I27M1D5M3I9M2I9M3D34M1I21M1D15M1I9M1I2M1I2M1I8M1I26M3D4M1D3M1I2M1I25M1I1M1I14M6I45M2I21M1I17M2D23M1D6M2I8M2D20M1I24M1D9M1I1M2D6M1D3M1D9M8I4M2I30M2D8M1D7M1I50M1I3M3I26M3D17M1D17M1D5M1D8M1I29M2D2M1I3M1I6M1D11M3I20M3I19M1I17M2I33M1D35M2D7M2D3M18D1M3D10M5D11M1D8M1D6M1I9M1I4M2D5M1D13M1D22M1D16M14I22M1D3M1I19M1D53M1I13M1I20M8I8M1I6M6D28M3D28M9D23M5D26M1I6M1D5M1D24M1I5M2I13M1I2M4I2M1I4M4I8M1I14M1I12M1I28M1I18M4I10M2D8M1I62M1I14M2I5M1I18M1D1M3I4M1I13M1D4M2I3M1D8M4D2M8D71M1I8M4I23M1I15M5D13M1D6M1D8M7I16M2I13M2D27M1D46M1I20M2D6M1I9M1D4M1I7M1D6M1I2M6I11M4D25M1I22M1D14M2D20M1D30M3I7M3D4M1I22M1D4M1D10M1D20M1I21M3I3M1I8M1D14M1I10M2I45M1D14M1D17M1D27M2D3M1I2M2I4M1D13M1D5M4I6M2I11M1I11M4I6M1I15M1I8M1I6M9I1M1I19M1I4M1I8M2D9M1I7M1D33M1D19M1D3M1D35M3D4M1D6M2D16M3D1M1D30M26D28M1D7M2I12M2D10M1I7M1D16M1D4M1I18M1I33M1I31M1I7M1I12M1D7M1D16M5I3M1I4M1D4M1D28M8D12M1D4M1D7M3D11M1D15M1D12M1I12M3I6M2D4M1D16M1I11M1D5M1D2M2I22M4D14M2I19M1D7M3I17M1I22M5D6M1D14M2D1M1D12M1I11M10I16M1D21M1D24M5D17M1D48M1D3M1D4M1D12M1D13M4D9M1I22M1I21M1I12M1D11M3D2M1D9M1I10M1D4M1I4M1D18M1I3M1D18M2D4M1I21M4D5M3I3M1D21M1I33M1D19M1I38M2I27M1I7M1I15M2I8M5D2M1D15M1I7M2I2M1I11M1D24M1I4M1D14M1I51M1D47M1D3M4D4M3D3M1I3M1D13M1D3M1I13M1I10M3I34M1D3M1I17M1D5M1I8M1D28M1I13M2I2M1I16M1D21M2I22M5I8M1I3M1I9M1D12M2D11M1I7M1I2M2D10M3I26M4D12M1D3M1D12M7I12M1I5M1D5M8D5M1D8M1I31M1D3M1D6M1I12M2D4M1D24M2I10M1I17M1D1M3D11M1D8M2D16M1D18M2D3M6D2M1D6M24D10M2I14M1I11M1I4M1D10M1I34M4I14M1D21M1D6M43D8M4D2M1D12M1D7M5D4M2I15M1D39M1D6M1I9M3D1M3D2M2D4M4D2M3D1M1D2M1D10M1I16M3D17M1I1M1I28M1D10M1D11M1D28M1D11M2I17M1I14M1I7M2D6M1D4M7D3M7D10M1I6M1I57M2D4M1D5M1D18M2I50M5I38M1D6M1D15M1D5M1I58M4I28M1I15M1D14M3I4M2D4M1I11M4D4M1D44M1I25M1I8M2D12M1I7M1D31M1D9M26I5M1I19M1D1M1D9M1D5M1D7M34I1M1I38M1I1M1I21M1D4M11D29M1D11M1D7M3I19M2I36M1D12M1I21M1I2M7I23M2I19M1I6M1I16M2I2M3D10M1D11M10I5M1I15M2D18M1I17M1I7M2D6M2I6M1D27M1I17M1I23M5I29M4D3M1I41M1D33M1D9M1D11M6I25M1D17M3D6M1I8M1I14M1D13M1D12M1I16M1I12M1I3M1D12M1I28M1D32M1D15M1I32M6I2M2I8M1D6M1D23M22I30M1I9M10D58M3I7M1D12M1I10M6I31M1D14M1I38M1I13M3D14M1D23M1I6M1I10M3I22M1I10M1I8M5I67M1I13M4D3M5D6M1I4M1I8M3D8M3I2M1I11M1D11M1I4M2I1M1I2M1I5M3I9M2D1M1D4M1D6M2D5M1D5M1I8M4D8M1I7M2I3M3D15M6D1M1D9M1D4M1D6M1D36M1D7M1D18M1I5M1D3M2I20M1D13M4I7M5I2M2I43M1I5M1D12M1I7M1D31M1I13M1D13M1I6M1D1M1D4M3D7M1D31M2D26M1I7M1I8M1D7M1I17M1D18M1I6M1D4M7D13M1I6M1D7M1I31M1D5M1I15M1D20M1I20M1I26M3I2M3I1M9I5M1I24M2D25M1D14M1D5M3D2M1I7M1I3M1I19M1I17M1I16M2I5M5D8M1I15M1I3M2I5M5I15M1D13M3D7M1D9M5I10M2D5M1I10M2I1M1I2M1I9M8I2M1D5M1I6M6D7M1I13M3I7M1I3M1D15M2D18M1D3M1D2M1D5M1D5M2I9M1I1M1I27M1I11M1D16M8I1M2I8M1I15M1I6M1I10M1D24M1D3M1D19M1I12M1I24M1D8M1D2M1D2M1I6M1D31M2I5M5D16M5I5M1I6M3D11M14D12M3I29M1I12M1I5M23I2M1I4M4I6M1D41M2I21M1D17M1D5M1D25M3I18M1D6M1D5M1D42M1I3M1D31M1I3M1D14M1D21M1I8M3D4M1I19M6D10M2I12M7I32M8I2M1D18M2D31M1D15M1I21M1I6M1I3M1I39M2I1M1D10M1D3M1I36M12D45M1D7M1I4M1I1M3I7M1I3M1D5M1D6M1D14M1D14M1I18M1D1M1D6M1I1M2D1M1D4M2D8M1D27M5I20M12D11M1D9M1D29M3D26M2D4M2D3M1I6M37D1M1D4M5D3M1D3M6D3M4D16M1D27M2D3M1D2M2D60M4D5M4I8M21D26M1D16M1D3M1I8M1D22M1I8M10D3M2D3M3D13M36D4M1D40M1I6M1I5M1I7M2I7M1I13M2I2M1D8M2I6M1I9M1I3M1D4M4I3M1D5M1I11M1D4M4D23M1I21M1I17M1D37M2I10M1D36M1D8M1D1M1D9M1I6M1D1M5D1M7D3M2D2M10D2M2D12M1I27M2I1M1D16M1D18M1D25M1D29M1I12M2I18M1I2M3I3M7I13M1D30M3D2M2D18M1D4M2D36M1I19M1D19M1I6M1I4M3D20M2D13M1I61M1I12M3D1M1D6M2D4M2D3M1I7M1D34M1I9M1D5M5D9M3D11M1D4M1I4M1I3M4D2M3D1M8D22M1I10M1D12M1D57M1D25M1D58M4I26M1I2M1I2M1I7M2I43M1I3M1D6M1D9M2D20M1D5M41D5M1D30M1D32M1D12M2I9M4I17M2D44M1D2M1I29M14I1M1I17M1I8M1D27M4I14M1D9M1D4M1I6M1D12M5D26M3I2M1I2M1I18M
diff --git a/products/jbrowse-cli/src/commands/add-track.ts b/products/jbrowse-cli/src/commands/add-track.ts
index 27a5ccbd86..43f6779990 100644
--- a/products/jbrowse-cli/src/commands/add-track.ts
+++ b/products/jbrowse-cli/src/commands/add-track.ts
@@ -428,7 +428,7 @@ export default class AddTrack extends JBrowseCommand {
       /\.gff3?\.b?gz$/i.test(location) ||
       /\.vcf\.b?gz$/i.test(location) ||
       /\.bed\.b?gz$/i.test(location) ||
-      /\.ppaf\.b?gz$/i.test(location)
+      /\.pif\.b?gz$/i.test(location)
     ) {
       return {
         file: location,
@@ -546,10 +546,10 @@ export default class AddTrack extends JBrowseCommand {
         type: 'BedAdapter',
         bedLocation: makeLocation(location),
       }
-    } else if (/\.ppaf\.b?gz$/i.test(location)) {
+    } else if (/\.pif\.b?gz$/i.test(location)) {
       return {
         type: 'PairwiseIndexedPAFAdapter',
-        ppafGzLocation: makeLocation(location),
+        pifGzLocation: makeLocation(location),
         index: {
           location: makeLocation(index || `${location}.tbi`),
           indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
diff --git a/products/jbrowse-cli/src/commands/process-paf.test.ts b/products/jbrowse-cli/src/commands/create-pif.test.ts
similarity index 86%
rename from products/jbrowse-cli/src/commands/process-paf.test.ts
rename to products/jbrowse-cli/src/commands/create-pif.test.ts
index 7c6ab47434..fb3e26fe35 100644
--- a/products/jbrowse-cli/src/commands/process-paf.test.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.test.ts
@@ -9,9 +9,9 @@ import { setup } from '../testUtil'
 const base = path.join(__dirname, '..', '..', 'test', 'data')
 const simplePaf = path.join(base, 'volvox_inv_indels.paf')
 
-describe('process-paf', () => {
+describe('create-pif', () => {
   setup
-    .command(['process-paf', simplePaf])
+    .command(['create-pif', simplePaf])
     .it('processes volvox paf', async ctx => {
       let res = ''
       for (const obj of ctx.stdout) {
diff --git a/products/jbrowse-cli/src/commands/process-paf.ts b/products/jbrowse-cli/src/commands/create-pif.ts
similarity index 81%
rename from products/jbrowse-cli/src/commands/process-paf.ts
rename to products/jbrowse-cli/src/commands/create-pif.ts
index 49c9581921..dd6f3fd6db 100644
--- a/products/jbrowse-cli/src/commands/process-paf.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.ts
@@ -43,26 +43,26 @@ export function swapIndelCigar(cigar: string) {
   return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
 }
 
-export default class ProcessPAF extends JBrowseCommand {
-  static description = 'Pairwise index the PAF'
+export default class CreatePIF extends JBrowseCommand {
+  static description = 'Create pairwise indexed PAF file (PIF)'
 
   static examples = [
-    '# processes a local PAF file into our custom format PPAF, which pairwise indexes the PAF',
+    '# processes a local PAF file into our custom format, PIF (pairwise indexed PAF)',
     '',
     '# read from stdin. could also pipe directly from minimap2 here',
-    '$ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.ppaf.gz',
-    '$ tabix out.ppaf.gz',
-    '$ jbrowse add-track out.ppaf.gz -a mm39,hg38',
+    '$ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.pif.gz',
+    '$ tabix out.pif.gz',
+    '$ jbrowse add-track out.pif.gz -a mm39,hg38',
     '',
     '# read from file instead of stdin',
-    '$ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.ppaf.gz',
-    '$ tabix out.ppaf.gz',
-    '$ jbrowse add-track out.ppaf.gz -a mm39,hg38',
+    '$ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.pif.gz',
+    '$ tabix out.pif.gz',
+    '$ jbrowse add-track out.pif.gz -a mm39,hg38',
   ]
 
   static args = {
     track: Args.string({
-      description: `Track file or URL (optional, stdin if not specified)`,
+      description: `Track file (optional, reads from stdin if not specified)`,
     }),
   }
 
@@ -71,7 +71,7 @@ export default class ProcessPAF extends JBrowseCommand {
   }
 
   async run() {
-    const { args: runArgs } = await this.parse(ProcessPAF)
+    const { args: runArgs } = await this.parse(CreatePIF)
     const { track: filename } = runArgs
 
     const rl1 = filename ? getReadline(filename) : getStdReadline()
diff --git a/products/jbrowse-cli/src/commands/create-pifgz.test.ts b/products/jbrowse-cli/src/commands/create-pifgz.test.ts
new file mode 100644
index 0000000000..b5661ed115
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/create-pifgz.test.ts
@@ -0,0 +1,20 @@
+/**
+ * @jest-environment node
+ */
+
+import path, { basename } from 'path'
+import fs from 'fs'
+import { setup } from '../testUtil'
+
+const base = path.join(__dirname, '..', '..', 'test', 'data')
+const simplePaf = path.join(base, 'volvox_inv_indels.paf')
+
+const exists = (p: string) => fs.existsSync(p)
+
+describe('create-pif', () => {
+  setup
+    .command(['create-pifgz', simplePaf])
+    .it('processes volvox paf', async ctx => {
+      expect(exists(basename(simplePaf, '.paf') + '.pif.gz')).toBeTruthy()
+    })
+})
diff --git a/products/jbrowse-cli/src/commands/create-pifgz.ts b/products/jbrowse-cli/src/commands/create-pifgz.ts
new file mode 100644
index 0000000000..84b83ad0e2
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/create-pifgz.ts
@@ -0,0 +1,64 @@
+import { Args, Flags } from '@oclif/core'
+import { sync as commandExistsSync } from 'command-exists'
+
+import { spawn } from 'child_process'
+import path from 'path'
+
+import JBrowseCommand from '../base'
+
+export default class CreatePifGz extends JBrowseCommand {
+  static description =
+    'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep'
+
+  static examples = [
+    '# sort gff and pipe to bgzip',
+    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
+    '$ tabix sorted.gff.gz',
+  ]
+
+  static args = {
+    file: Args.string({
+      required: true,
+      description: `GFF file`,
+    }),
+    out: Args.string({
+      description:
+        'Where to write the output file. If unspecified, will be ${file}.pif.gz',
+    }),
+  }
+
+  static flags = {
+    help: Flags.help({ char: 'h' }),
+  }
+
+  async run() {
+    const {
+      args: { file, out },
+    } = await this.parse(CreatePifGz)
+
+    if (
+      commandExistsSync('sh') &&
+      commandExistsSync('sort') &&
+      commandExistsSync('grep') &&
+      commandExistsSync('tabix') &&
+      commandExistsSync('bgzip')
+    ) {
+      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+      spawn(
+        'sh',
+        [
+          '-c',
+          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+        ],
+        {
+          env: { ...process.env, LC_ALL: 'C' },
+          stdio: 'inherit',
+        },
+      )
+    } else {
+      throw new Error(
+        'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
+      )
+    }
+  }
+}
diff --git a/test_data/hs1_vs_mm39/config.json b/test_data/hs1_vs_mm39/config.json
index 15b8e1ff2b..2ec8f875c1 100644
--- a/test_data/hs1_vs_mm39/config.json
+++ b/test_data/hs1_vs_mm39/config.json
@@ -107,11 +107,11 @@
     },
     {
       "type": "SyntenyTrack",
-      "trackId": "hs1ToMm39.over.chain.ppaf",
-      "name": "hs1ToMm39.over.chain.ppaf",
+      "trackId": "hs1ToMm39.over.chain.pif",
+      "name": "hs1ToMm39.over.chain.pif",
       "adapter": {
         "type": "PairwiseIndexedPAFAdapter",
-        "ppafGzLocation": {
+        "pifGzLocation": {
           "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hs1_vs_mm39/hs1ToMm39.over.chain.ppaf.gz",
           "locationType": "UriLocation"
         },

From b03f81eaac58a45dae01f1d7437cb3e0ff73646a Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 09:18:27 -0500
Subject: [PATCH 08/12] Remove separation between create-pif and create-pifgz

---
 products/jbrowse-cli/README.md                |  10 +-
 .../src/commands/create-pif.test.ts           |  16 +--
 .../jbrowse-cli/src/commands/create-pif.ts    | 130 +++++++-----------
 .../src/commands/create-pifgz.test.ts         |  20 ---
 .../jbrowse-cli/src/commands/create-pifgz.ts  |  64 ---------
 .../jbrowse-cli/src/commands/pif-utils.ts     |  64 +++++++++
 6 files changed, 123 insertions(+), 181 deletions(-)
 delete mode 100644 products/jbrowse-cli/src/commands/create-pifgz.test.ts
 delete mode 100644 products/jbrowse-cli/src/commands/create-pifgz.ts
 create mode 100644 products/jbrowse-cli/src/commands/pif-utils.ts

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index 0f88a79d58..1e5ee371e7 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -54,7 +54,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
 - [`jbrowse create-pif [TRACK]`](#jbrowse-create-pif-track)
-- [`jbrowse create-pifgz FILE [OUTPUT]`](#jbrowse-create-pifgz-file-output)
+- [`jbrowse create-pifgz FILE [OUT]`](#jbrowse-create-pifgz-file-out)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
@@ -503,7 +503,7 @@ EXAMPLES
 _See code:
 [src/commands/create-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pif.ts)_
 
-## `jbrowse create-pifgz FILE [OUTPUT]`
+## `jbrowse create-pifgz FILE [OUT]`
 
 Helper utility to sort GFF files for tabix. Moves all lines starting with # to
 the top of the file, and sort by refname and start position using unix utilities
@@ -511,11 +511,11 @@ sort and grep
 
 ```
 USAGE
-  $ jbrowse create-pifgz FILE [OUTPUT] [-h]
+  $ jbrowse create-pifgz FILE [OUT] [-h]
 
 ARGUMENTS
-  FILE    GFF file
-  OUTPUT  Where to write the output file. If unspecified, will be ${file}.pif.gz
+  FILE  GFF file
+  OUT   Where to write the output file. If unspecified, will be ${file}.pif.gz
 
 FLAGS
   -h, --help  Show CLI help.
diff --git a/products/jbrowse-cli/src/commands/create-pif.test.ts b/products/jbrowse-cli/src/commands/create-pif.test.ts
index fb3e26fe35..ae731c97bf 100644
--- a/products/jbrowse-cli/src/commands/create-pif.test.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.test.ts
@@ -3,21 +3,19 @@
  */
 
 import path from 'path'
-
+import fs from 'fs'
 import { setup } from '../testUtil'
 
 const base = path.join(__dirname, '..', '..', 'test', 'data')
 const simplePaf = path.join(base, 'volvox_inv_indels.paf')
 
+const exists = (p: string) => fs.existsSync(p)
+
 describe('create-pif', () => {
+  const fn = path.basename(simplePaf, '.paf') + '.pif.gz'
   setup
-    .command(['create-pif', simplePaf])
-    .it('processes volvox paf', async ctx => {
-      let res = ''
-      for (const obj of ctx.stdout) {
-        res += obj[0]
-      }
-      expect(res.split('\n').length).toBe(15)
-      expect(res).toMatchSnapshot()
+    .command(['create-pifgz', simplePaf, '--out', fn])
+    .it('processes volvox paf', () => {
+      expect(exists(fn)).toBeTruthy()
     })
 })
diff --git a/products/jbrowse-cli/src/commands/create-pif.ts b/products/jbrowse-cli/src/commands/create-pif.ts
index dd6f3fd6db..5980e92e25 100644
--- a/products/jbrowse-cli/src/commands/create-pif.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.ts
@@ -1,103 +1,67 @@
-import fs from 'fs'
-import JBrowseCommand from '../base'
-
-import readline from 'readline'
-import { createGunzip } from 'zlib'
 import { Args, Flags } from '@oclif/core'
+import { sync as commandExistsSync } from 'command-exists'
 
-function getReadline(filename: string) {
-  const stream = fs.createReadStream(filename)
-  return readline.createInterface({
-    input: filename.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
-  })
-}
-
-function getStdReadline() {
-  return readline.createInterface({
-    input: process.stdin,
-  })
-}
-
-const cigarRegex = new RegExp(/([MIDNSHPX=])/)
-
-export function parseCigar(cigar = '') {
-  return cigar.split(cigarRegex).slice(0, -1)
-}
-export function flipCigar(cigar: string[]) {
-  const arr = []
-  for (let i = cigar.length - 2; i >= 0; i -= 2) {
-    arr.push(cigar[i])
-    const op = cigar[i + 1]
-    if (op === 'D') {
-      arr.push('I')
-    } else if (op === 'I') {
-      arr.push('D')
-    } else {
-      arr.push(op)
-    }
-  }
-  return arr
-}
+import { spawn } from 'child_process'
+import path from 'path'
 
-export function swapIndelCigar(cigar: string) {
-  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
-}
+import JBrowseCommand from '../base'
 
-export default class CreatePIF extends JBrowseCommand {
-  static description = 'Create pairwise indexed PAF file (PIF)'
+export default class CreatePif extends JBrowseCommand {
+  static description =
+    'creates pairwise indexed PAF (PIF), with bgzip and tabix'
 
   static examples = [
-    '# processes a local PAF file into our custom format, PIF (pairwise indexed PAF)',
+    '$ jbrowse create-pifgz input.paf # creates input.pif.gz in same directory',
     '',
-    '# read from stdin. could also pipe directly from minimap2 here',
-    '$ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.pif.gz',
-    '$ tabix out.pif.gz',
-    '$ jbrowse add-track out.pif.gz -a mm39,hg38',
-    '',
-    '# read from file instead of stdin',
-    '$ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.pif.gz',
-    '$ tabix out.pif.gz',
-    '$ jbrowse add-track out.pif.gz -a mm39,hg38',
+    '$ jbrowse create-pifgz input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
   ]
 
-  static args = {
-    track: Args.string({
-      description: `Track file (optional, reads from stdin if not specified)`,
-    }),
-  }
-
   static flags = {
+    out: Flags.string({
+      description:
+        'Where to write the output file. If unspecified, will be ${file}.pif.gz',
+    }),
+    csi: Flags.string({
+      description: 'Create a CSI index for the PIF file instead of TBI',
+    }),
     help: Flags.help({ char: 'h' }),
   }
+  static args = {
+    file: Args.string({
+      required: true,
+      description: `PAF file as input`,
+    }),
+  }
 
   async run() {
-    const { args: runArgs } = await this.parse(CreatePIF)
-    const { track: filename } = runArgs
-
-    const rl1 = filename ? getReadline(filename) : getStdReadline()
-    for await (const line of rl1) {
-      const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
+    const {
+      args: { file },
+      flags: { out },
+    } = await this.parse(CreatePif)
 
-      process.stdout.write(
-        [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') +
-          '\n',
+    if (
+      commandExistsSync('sh') &&
+      commandExistsSync('sort') &&
+      commandExistsSync('grep') &&
+      commandExistsSync('tabix') &&
+      commandExistsSync('bgzip')
+    ) {
+      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+      spawn(
+        'sh',
+        [
+          '-c',
+          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+        ],
+        {
+          env: { ...process.env, LC_ALL: 'C' },
+          stdio: 'inherit',
+        },
       )
-      const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
-
-      const CIGAR = rest[cigarIdx]
-      if (CIGAR) {
-        rest[cigarIdx] = `cg:Z:${
-          strand === '-'
-            ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
-            : swapIndelCigar(CIGAR.slice(5))
-        }`
-      }
-
-      process.stdout.write(
-        [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') +
-          '\n',
+    } else {
+      throw new Error(
+        'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
       )
     }
-    rl1.close()
   }
 }
diff --git a/products/jbrowse-cli/src/commands/create-pifgz.test.ts b/products/jbrowse-cli/src/commands/create-pifgz.test.ts
deleted file mode 100644
index b5661ed115..0000000000
--- a/products/jbrowse-cli/src/commands/create-pifgz.test.ts
+++ /dev/null
@@ -1,20 +0,0 @@
-/**
- * @jest-environment node
- */
-
-import path, { basename } from 'path'
-import fs from 'fs'
-import { setup } from '../testUtil'
-
-const base = path.join(__dirname, '..', '..', 'test', 'data')
-const simplePaf = path.join(base, 'volvox_inv_indels.paf')
-
-const exists = (p: string) => fs.existsSync(p)
-
-describe('create-pif', () => {
-  setup
-    .command(['create-pifgz', simplePaf])
-    .it('processes volvox paf', async ctx => {
-      expect(exists(basename(simplePaf, '.paf') + '.pif.gz')).toBeTruthy()
-    })
-})
diff --git a/products/jbrowse-cli/src/commands/create-pifgz.ts b/products/jbrowse-cli/src/commands/create-pifgz.ts
deleted file mode 100644
index 84b83ad0e2..0000000000
--- a/products/jbrowse-cli/src/commands/create-pifgz.ts
+++ /dev/null
@@ -1,64 +0,0 @@
-import { Args, Flags } from '@oclif/core'
-import { sync as commandExistsSync } from 'command-exists'
-
-import { spawn } from 'child_process'
-import path from 'path'
-
-import JBrowseCommand from '../base'
-
-export default class CreatePifGz extends JBrowseCommand {
-  static description =
-    'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep'
-
-  static examples = [
-    '# sort gff and pipe to bgzip',
-    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
-    '$ tabix sorted.gff.gz',
-  ]
-
-  static args = {
-    file: Args.string({
-      required: true,
-      description: `GFF file`,
-    }),
-    out: Args.string({
-      description:
-        'Where to write the output file. If unspecified, will be ${file}.pif.gz',
-    }),
-  }
-
-  static flags = {
-    help: Flags.help({ char: 'h' }),
-  }
-
-  async run() {
-    const {
-      args: { file, out },
-    } = await this.parse(CreatePifGz)
-
-    if (
-      commandExistsSync('sh') &&
-      commandExistsSync('sort') &&
-      commandExistsSync('grep') &&
-      commandExistsSync('tabix') &&
-      commandExistsSync('bgzip')
-    ) {
-      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
-      spawn(
-        'sh',
-        [
-          '-c',
-          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
-        ],
-        {
-          env: { ...process.env, LC_ALL: 'C' },
-          stdio: 'inherit',
-        },
-      )
-    } else {
-      throw new Error(
-        'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
-      )
-    }
-  }
-}
diff --git a/products/jbrowse-cli/src/commands/pif-utils.ts b/products/jbrowse-cli/src/commands/pif-utils.ts
new file mode 100644
index 0000000000..b9afcc725b
--- /dev/null
+++ b/products/jbrowse-cli/src/commands/pif-utils.ts
@@ -0,0 +1,64 @@
+import fs from 'fs'
+
+import readline from 'readline'
+import { createGunzip } from 'zlib'
+
+function getReadline(filename: string) {
+  const stream = fs.createReadStream(filename)
+  return readline.createInterface({
+    input: filename.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
+  })
+}
+
+function getStdReadline() {
+  return readline.createInterface({
+    input: process.stdin,
+  })
+}
+
+const cigarRegex = new RegExp(/([MIDNSHPX=])/)
+
+export function parseCigar(cigar = '') {
+  return cigar.split(cigarRegex).slice(0, -1)
+}
+export function flipCigar(cigar: string[]) {
+  const arr = []
+  for (let i = cigar.length - 2; i >= 0; i -= 2) {
+    arr.push(cigar[i])
+    const op = cigar[i + 1]
+    if (op === 'D') {
+      arr.push('I')
+    } else if (op === 'I') {
+      arr.push('D')
+    } else {
+      arr.push(op)
+    }
+  }
+  return arr
+}
+
+export async function createPIF(filename?: string) {
+  const rl1 = filename ? getReadline(filename) : getStdReadline()
+  for await (const line of rl1) {
+    const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
+
+    process.stdout.write(
+      [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n',
+    )
+    const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
+
+    const CIGAR = rest[cigarIdx]
+    if (CIGAR) {
+      rest[cigarIdx] = `cg:Z:${
+        strand === '-'
+          ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
+          : swapIndelCigar(CIGAR.slice(5))
+      }`
+    }
+
+    process.stdout.write(
+      [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n',
+    )
+  }
+  rl1.close()
+}

From 522851fb8b376adcc18af6d35ea3deb22436ce20 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 09:22:45 -0500
Subject: [PATCH 09/12] Misc

---
 .gitignore                                    |   1 -
 products/jbrowse-cli/README.md                |  69 ++-------
 .../src/commands/create-pif.test.ts           |   2 +-
 .../jbrowse-cli/src/commands/create-pif.ts    | 137 ++++++++++++++----
 .../jbrowse-cli/src/commands/pif-utils.ts     |  64 --------
 5 files changed, 117 insertions(+), 156 deletions(-)
 delete mode 100644 products/jbrowse-cli/src/commands/pif-utils.ts

diff --git a/.gitignore b/.gitignore
index 7322edaaad..5a3a883bc7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,4 +19,3 @@ lerna-debug.log
 .yarn
 .yarnrc
 *.tsbuildinfo
-products/jbrowse-cli/test/data/volvox_inv_indels.paf.pif.gz*
diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index 1e5ee371e7..af57958da3 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -53,8 +53,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track)
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
-- [`jbrowse create-pif [TRACK]`](#jbrowse-create-pif-track)
-- [`jbrowse create-pifgz FILE [OUT]`](#jbrowse-create-pifgz-file-out)
+- [`jbrowse create-pif FILE`](#jbrowse-create-pif-file)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
@@ -459,82 +458,36 @@ EXAMPLES
 _See code:
 [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse create-pif [TRACK]`
+## `jbrowse create-pif FILE`
 
-Create pairwise indexed PAF file (PIF)
+creates pairwise indexed PAF (PIF), with bgzip and tabix
 
 ```
 USAGE
-  $ jbrowse create-pif [TRACK] [-h]
+  $ jbrowse create-pif FILE [--out <value>] [--csi <value>] [-h]
 
 ARGUMENTS
-  TRACK  Track file (optional, reads from stdin if not specified)
+  FILE  PAF file as input
 
 FLAGS
-  -h, --help  Show CLI help.
+  -h, --help         Show CLI help.
+      --csi=<value>  Create a CSI index for the PIF file instead of TBI
+      --out=<value>  Where to write the output file. If unspecified, will be ${file}.pif.gz
 
 DESCRIPTION
-  Create pairwise indexed PAF file (PIF)
+  creates pairwise indexed PAF (PIF), with bgzip and tabix
 
 EXAMPLES
-  # processes a local PAF file into our custom format, PIF (pairwise indexed PAF)
-
-
-
-  # read from stdin. could also pipe directly from minimap2 here
-
-  $ cat file.paf | jbrowse process-paf | sort -k1,1 -k3,3n | bgzip > out.pif.gz
-
-  $ tabix out.pif.gz
-
-  $ jbrowse add-track out.pif.gz -a mm39,hg38
-
-
-
-  # read from file instead of stdin
+  $ jbrowse create-pif input.paf # creates input.pif.gz in same directory
 
-  $ jbrowse process-paf file.paf | sort -k1,1 -k3,3n | bgzip >  out.pif.gz
 
-  $ tabix out.pif.gz
 
-  $ jbrowse add-track out.pif.gz -a mm39,hg38
+  $ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
 ```
 
 _See code:
 [src/commands/create-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pif.ts)_
 
-## `jbrowse create-pifgz FILE [OUT]`
-
-Helper utility to sort GFF files for tabix. Moves all lines starting with # to
-the top of the file, and sort by refname and start position using unix utilities
-sort and grep
-
-```
-USAGE
-  $ jbrowse create-pifgz FILE [OUT] [-h]
-
-ARGUMENTS
-  FILE  GFF file
-  OUT   Where to write the output file. If unspecified, will be ${file}.pif.gz
-
-FLAGS
-  -h, --help  Show CLI help.
-
-DESCRIPTION
-  Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
-  refname and start position using unix utilities sort and grep
-
-EXAMPLES
-  # sort gff and pipe to bgzip
-
-  $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
-
-  $ tabix sorted.gff.gz
-```
-
-_See code:
-[src/commands/create-pifgz.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pifgz.ts)_
-
 ## `jbrowse help [COMMANDS]`
 
 Display help for jbrowse.
diff --git a/products/jbrowse-cli/src/commands/create-pif.test.ts b/products/jbrowse-cli/src/commands/create-pif.test.ts
index ae731c97bf..6de1367302 100644
--- a/products/jbrowse-cli/src/commands/create-pif.test.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.test.ts
@@ -14,7 +14,7 @@ const exists = (p: string) => fs.existsSync(p)
 describe('create-pif', () => {
   const fn = path.basename(simplePaf, '.paf') + '.pif.gz'
   setup
-    .command(['create-pifgz', simplePaf, '--out', fn])
+    .command(['create-pif', simplePaf, '--out', fn])
     .it('processes volvox paf', () => {
       expect(exists(fn)).toBeTruthy()
     })
diff --git a/products/jbrowse-cli/src/commands/create-pif.ts b/products/jbrowse-cli/src/commands/create-pif.ts
index 5980e92e25..7287b9e87d 100644
--- a/products/jbrowse-cli/src/commands/create-pif.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.ts
@@ -1,19 +1,86 @@
+import fs from 'fs'
+import readline from 'readline'
+import { createGunzip } from 'zlib'
 import { Args, Flags } from '@oclif/core'
 import { sync as commandExistsSync } from 'command-exists'
-
 import { spawn } from 'child_process'
 import path from 'path'
 
 import JBrowseCommand from '../base'
 
-export default class CreatePif extends JBrowseCommand {
+const cigarRegex = new RegExp(/([MIDNSHPX=])/)
+
+function getReadline(filename: string) {
+  const stream = fs.createReadStream(filename)
+  return readline.createInterface({
+    input: filename.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
+  })
+}
+
+function getStdReadline() {
+  return readline.createInterface({
+    input: process.stdin,
+  })
+}
+
+function parseCigar(cigar = '') {
+  return cigar.split(cigarRegex).slice(0, -1)
+}
+
+export function flipCigar(cigar: string[]) {
+  const arr = []
+  for (let i = cigar.length - 2; i >= 0; i -= 2) {
+    arr.push(cigar[i])
+    const op = cigar[i + 1]
+    if (op === 'D') {
+      arr.push('I')
+    } else if (op === 'I') {
+      arr.push('D')
+    } else {
+      arr.push(op)
+    }
+  }
+  return arr
+}
+
+export function swapIndelCigar(cigar: string) {
+  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
+}
+
+export async function createPIF(filename?: string, child: { stdin: any }) {
+  const rl1 = filename ? getReadline(filename) : getStdReadline()
+  for await (const line of rl1) {
+    const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
+
+    child.stdin.write(
+      [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n',
+    )
+    const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
+
+    const CIGAR = rest[cigarIdx]
+    if (CIGAR) {
+      rest[cigarIdx] = `cg:Z:${
+        strand === '-'
+          ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
+          : swapIndelCigar(CIGAR.slice(5))
+      }`
+    }
+
+    child.stdin.write(
+      [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n',
+    )
+  }
+  rl1.close()
+}
+
+export default class CreatePIF extends JBrowseCommand {
   static description =
     'creates pairwise indexed PAF (PIF), with bgzip and tabix'
 
   static examples = [
-    '$ jbrowse create-pifgz input.paf # creates input.pif.gz in same directory',
+    '$ jbrowse create-pif input.paf # creates input.pif.gz in same directory',
     '',
-    '$ jbrowse create-pifgz input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
+    '$ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
   ]
 
   static flags = {
@@ -34,34 +101,40 @@ export default class CreatePif extends JBrowseCommand {
   }
 
   async run() {
-    const {
-      args: { file },
-      flags: { out },
-    } = await this.parse(CreatePif)
-
-    if (
-      commandExistsSync('sh') &&
-      commandExistsSync('sort') &&
-      commandExistsSync('grep') &&
-      commandExistsSync('tabix') &&
-      commandExistsSync('bgzip')
-    ) {
-      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
-      spawn(
-        'sh',
-        [
-          '-c',
-          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
-        ],
-        {
-          env: { ...process.env, LC_ALL: 'C' },
-          stdio: 'inherit',
-        },
-      )
-    } else {
-      throw new Error(
-        'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
-      )
+    try {
+      const {
+        args: { file },
+        flags: { out, csi },
+      } = await this.parse(CreatePIF)
+
+      if (
+        commandExistsSync('sh') &&
+        commandExistsSync('sort') &&
+        commandExistsSync('grep') &&
+        commandExistsSync('tabix') &&
+        commandExistsSync('bgzip')
+      ) {
+        const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+        console.error('start')
+        const child = spawn(
+          'sh',
+          [
+            '-c',
+            `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+          ],
+          {
+            env: { ...process.env, LC_ALL: 'C' },
+            stdio: 'inherit',
+          },
+        )
+        await createPIF(fn, child)
+      } else {
+        throw new Error(
+          'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
+        )
+      }
+    } catch (e) {
+      console.error(e)
     }
   }
 }
diff --git a/products/jbrowse-cli/src/commands/pif-utils.ts b/products/jbrowse-cli/src/commands/pif-utils.ts
deleted file mode 100644
index b9afcc725b..0000000000
--- a/products/jbrowse-cli/src/commands/pif-utils.ts
+++ /dev/null
@@ -1,64 +0,0 @@
-import fs from 'fs'
-
-import readline from 'readline'
-import { createGunzip } from 'zlib'
-
-function getReadline(filename: string) {
-  const stream = fs.createReadStream(filename)
-  return readline.createInterface({
-    input: filename.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
-  })
-}
-
-function getStdReadline() {
-  return readline.createInterface({
-    input: process.stdin,
-  })
-}
-
-const cigarRegex = new RegExp(/([MIDNSHPX=])/)
-
-export function parseCigar(cigar = '') {
-  return cigar.split(cigarRegex).slice(0, -1)
-}
-export function flipCigar(cigar: string[]) {
-  const arr = []
-  for (let i = cigar.length - 2; i >= 0; i -= 2) {
-    arr.push(cigar[i])
-    const op = cigar[i + 1]
-    if (op === 'D') {
-      arr.push('I')
-    } else if (op === 'I') {
-      arr.push('D')
-    } else {
-      arr.push(op)
-    }
-  }
-  return arr
-}
-
-export async function createPIF(filename?: string) {
-  const rl1 = filename ? getReadline(filename) : getStdReadline()
-  for await (const line of rl1) {
-    const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
-
-    process.stdout.write(
-      [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n',
-    )
-    const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
-
-    const CIGAR = rest[cigarIdx]
-    if (CIGAR) {
-      rest[cigarIdx] = `cg:Z:${
-        strand === '-'
-          ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
-          : swapIndelCigar(CIGAR.slice(5))
-      }`
-    }
-
-    process.stdout.write(
-      [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n',
-    )
-  }
-  rl1.close()
-}

From 1f3ca2d337aec396f06ee0ee5efc9d09280ec015 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 09:41:15 -0500
Subject: [PATCH 10/12] Misc

---
 .../__snapshots__/create-pif.test.ts.snap     | 20 ++---
 .../src/commands/create-pif.test.ts           |  2 +
 .../jbrowse-cli/src/commands/create-pif.ts    | 78 ++++++++++---------
 3 files changed, 53 insertions(+), 47 deletions(-)

diff --git a/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
index bb837cbf18..da66ddcf40 100644
--- a/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
+++ b/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
@@ -1,19 +1,19 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`create-pif processes volvox paf 1`] = `
-"tctgA	50001	27258	50001	+	ctgA	49186	26805	49184	20447	24398	60	NM:i:3951	ms:i:29302	AS:i:26545	nn:i:0	tp:A:P	cm:i:1101	s1:i:8814	s2:i:212	de:f:0.0807	zd:i:2	rl:i:0	cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2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+"qctgA	49186	3	1851	+	ctgA	50001	0	1859	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1D16M1D5M3D33M1I14M3I7M1I25M2D5M2D4M1I17M3I11M1I5M3I3M1D15M3D1M2D6M1D2M6I6M2I24M1D3M2I29M1D2M1D3M1D6M1D10M2I8M19I33M1I23M2I9M1I11M1D6M1I5M1I28M1D13M1I5M1D2M1D49M5I6M2D21M1I1M2I2M2I4M4D4M1D5M1D3M1I2M1D4M37I17M2D16M6I5M3I3M6I16M5D4M8D5M4D1M1D52M2I2M1D5M28I33M1I17M2D2M2I31M42D5M1D9M1D7M1I8M1D40M1D39M1D2M1I3M2D11M2D6M2D10M1I14M1D12M1D16M1I6M3D6M2D4M1D1M1D27M1D3M10D3M2I11M3I3M1D35M1D1M3I3M2I19M3I9M4I23M1D3M1D28M1D52M1D28M1I20M2D66M1D3M2D7M1I7M2I9M1I11M1I11M1I7M1D3M1D30M1I11M1I15M2D7M3I3M1D12M6D35M1I4M1I17M1I15M1D5M1I4M1D5M1D3M5I10M1I2M1I8M7D13M5D9M1I4M1D45M6D4M1D19M2I16M1I1M2D23M7D11M1D19M1I13M
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 qctgA	49186	2214	15925	+	ctgA	50001	2212	16198	12504	15030	60	NM:i:2526	ms:i:17647	AS:i:15934	nn:i:0	tp:A:P	cm:i:637	s1:i:5099	s2:i:212	de:f:0.0837	zd:i:3	rl:i:0	cg:Z:10M1D4M2D21M1D10M1D14M1D5M1I29M2I9M1D15M1D27M1D12M1I5M1D11M1I7M2D4M2I9M1I4M6I32M1I13M1D55M1D8M1D1M1D12M1D2M1I22M2D56M1I11M1D5M5D17M3D3M1D13M1I16M1D50M1D2M1D10M1I1M1I42M1I2M2I33M22D3M1D2M1D6M1I8M2I5M1I50M1I6M3I6M2I12M3D13M1I9M5I1M1I10M1D3M1I5M1D3M1D4M1D24M1D5M2I30M1I3M1D15M1I9M1D3M1D18M1D9M1I11M2I6M1D23M4I1M1I22M1D3M1D11M2I1M1I7M1I4M1I18M1D6M1D5M2I5M1D66M2D3M1I8M1D13M1D8M1D3M2I4M1I20M1D5M2D22M1D6M8D14M1D6M1I8M2I5M9I7M2D4M1I11M1D20M2I2M1D33M8D10M2D7M1D18M4D5M1I4M4I1M1I33M3D10M1I20M2I8M1I9M1D10M1I7M1D8M1I6M2D66M1D3M2D2M1D24M1I63M1D14M8D7M1D13M1I31M1D16M4I41M1I3M1I4M23D9M1I2M1I8M1D1M1D12M1D2M1D3M1I33M1D24M2D3M1D4M1D12M122I6M4I2M1I13M1D3M1I35M1D4M1D13M1I32M1I6M1D5M1D5M1I12M1I8M1I48M1D2M1I19M1I9M1D24M1I13M1I8M1D5M7D5M2I10M1D11M3D15M1D6M2D4M1D18M1I14M1I3M1I1M2I17M1I12M4I15M1D3M1I31M1I1M1I1M1I1M1I12M5D2M1I31M2D18M1I5M20I10M1D20M3I11M1D14M1D1M9D4M4D2M4D2M3D4M1I10M1I50M1D14M1D11M8D11M2I9M1D20M3D5M1D27M1I5M3D9M2D9M3I34M1D21M1I15M1D9M1D2M1D2M1D8M1D26M3I4M1I3M1D2M1D25M1D1M1D14M6D45M2D21M1D17M2I23M1I6M2D8M2I20M1D24M1I9M1D1M2I6M1I3M1I9M8D4M2D30M2I8M1I7M1D50M1D3M3D26M3I17M1I17M1I5M1I8M1D29M2I2M1D3M1D6M1I11M3D20M3D19M1D17M2D33M1I35M2I7M2I3M18I1M3I10M5I11M1I8M1I6M1D9M1D4M2I5M1I13M1I22M1I16M14D22M1I3M1D19M1I53M1D13M1D20M8D8M1D6M6I28M3I28M9I23M5I26M1D6M1I5M1I24M1D5M2D13M1D2M4D2M1D4M4D8M1D14M1D12M1D28M1D18M4D10M2I8M1D62M1D14M2D5M1D18M1I1M3D4M1D13M1I4M2D3M1I8M4I2M8I71M1D8M4D23M1D15M5I13M1I6M1I8M7D16M2D13M2I27M1I46M1D20M2I6M1D9M1I4M1D7M1I6M1D2M6D11M4I25M1D22M1I14M2I20M1I30M3D7M3I4M1D22M1I4M1I10M1I20M1D21M3D3M1D8M1I14M1D10M2D45M1I14M1I17M1I27M2I3M1D2M2D4M1I13M1I5M4D6M2D11M1D11M4D6M1D15M1D8M1D6M9D1M1D19M1D4M1D8M2I9M1D7M1I33M1I19M1I3M1I35M3I4M1I6M2I16M3I1M1I30M26I28M1I7M2D12M2I10M1D7M1I16M1I4M1D18M1D33M1D31M1D7M1D12M1I7M1I16M5D3M1D4M1I4M1I28M8I12M1I4M1I7M3I11M1I15M1I12M1D12M3D6M2I4M1I16M1D11M1I5M1I2M2D22M4I14M2D19M1I7M3D17M1D22M5I6M1I14M2I1M1I12M1D11M10D16M1I21M1I24M5I17M1I48M1I3M1I4M1I12M1I13M4I9M1D22M1D21M1D12M1I11M3I2M1I9M1D10M1I4M1D4M1I18M1D3M1I18M2I4M1D21M4I5M3D3M1I21M1D33M1I19M1D38M2D27M1D7M1D15M2D8M5I2M1I15M1D7M2D2M1D11M1I24M1D4M1I14M1D51M1I47M1I3M4I4M3I3M1D3M1I13M1I3M1D13M1D10M3D34M1I3M1D17M1I5M1D8M1I28M1D13M2D2M1D16M1I21M2D22M5D8M1D3M1D9M1I12M2I11M1D7M1D2M2I10M3D26M4I12M1I3M1I12M7D12M1D5M1I5M8I5M1I8M1D31M1I3M1I6M1D12M2I4M1I24M2D10M1D17M1I1M3I11M1I8M2I16M1I18M2I3M6I2M1I6M24I10M2D14M1D11M1D4M1I10M1D34M4D14M1I21M1I6M43I8M4I2M1I12M1I7M5I4M2D15M1I39M1I6M1D9M3I1M3I2M2I4M4I2M3I1M1I2M1I10M1D16M3I17M1D1M1D28M1I10M1I11M1I28M1I11M2D17M1D14M1D7M2I6M1I4M7I3M7I10M1D6M1D57M2I4M1I5M1I18M2D50M5D38M1I6M1I15M1I5M1D58M4D28M1D15M1I14M3D4M2I4M1D11M4I4M1I44M1D25M1D8M2I12M1D7M1I31M1I9M26D5M1D19M1I1M1I9M1I5M1I7M34D1M1D38M1D1M1D21M1I4M11I29M1I11M1I7M3D19M2D36M1I12M1D21M1D2M7D23M2D19M1D6M1D16M2D2M3I10M1I11M10D5M1D15M2I18M1D17M1D7M2I6M2D6M1I27M1D17M1D23M5D29M4I3M1D41M1I33M1I9M1I11M6D25M1I17M3I6M1D8M1D14M1I13M1I12M1D16M1D12M1D3M1I12M1D28M1I32M1I15M1D32M6D2M2D8M1I6M1I23M22D30M1D9M10I58M3D7M1I12M1D10M6D31M1I14M1D38M1D13M3I14M1I23M1D6M1D10M3D22M1D10M1D8M5D67M1D13M4I3M5I6M1D4M1D8M3I8M3D2M1D11M1I11M1D4M2D1M1D2M1D5M3D9M2I1M1I4M1I6M2I5M1I5M1D8M4I8M1D7M2D3M3I15M6I1M1I9M1I4M1I6M1I36M1I7M1I18M1D5M1I3M2D20M1I13M4D7M5D2M2D43M1D5M1I12M1D7M1I31M1D13M1I13M1D6M1I1M1I4M3I7M1I31M2I26M1D7M1D8M1I7M1D17M1I18M1D6M1I4M7I13M1D6M1I7M1D31M1I5M1D15M1I20M1D20M1D26M3D2M3D1M9D5M1D24M2I25M1I14M1I5M3I2M1D7M1D3M1D19M1D17M1D16M2D5M5I8M1D15M1D3M2D5M5D15M1I13M3I7M1I9M5D10M2I5M1D10M2D1M1D2M1D9M8D2M1I5M1D6M6I7M1D13M3D7M1D3M1I15M2I18M1I3M1I2M1I5M1I5M2D9M1D1M1D27M1D11M1I16M8D1M2D8M1D15M1D6M1D10M1I24M1I3M1I19M1D12M1D24M1I8M1I2M1I2M1D6M1I31M2D5M5I16M5D5M1D6M3I11M14I12M3D29M1D12M1D5M23D2M1D4M4D6M1I41M2D21M1I17M1I5M1I25M3D18M1I6M1I5M1I42M1D3M1I31M1D3M1I14M1I21M1D8M3I4M1D19M6I10M2D12M7D32M8D2M1I18M2I31M1I15M1D21M1D6M1D3M1D39M2D1M1I10M1I3M1D36M12I45M1I7M1D4M1D1M3D7M1D3M1I5M1I6M1I14M1I14M1D18M1I1M1I6M1D1M2I1M1I4M2I8M1I27M5D20M12I11M1I9M1I29M3I26M2I4M2I3M1D6M37I1M1I4M5I3M1I3M6I3M4I16M1I27M2I3M1I2M2I60M4I5M4D8M21I26M1I16M1I3M1D8M1I22M1D8M10I3M2I3M3I13M36I4M1I40M1D6M1D5M1D7M2D7M1D13M2D2M1I8M2D6M1D9M1D3M1I4M4D3M1I5M1D11M1I4M4I23M1D21M1D17M1I37M2D10M1I36M1I8M1I1M1I9M1D6M1I1M5I1M7I3M2I2M10I2M2I12M1D27M2D1M1I16M1I18M1I25M1I29M1D12M2D18M1D2M3D3M7D13M1I30M3I2M2I18M1I4M2I36M1D19M1I19M1D6M1D4M3I20M2I13M1D61M1D12M3I1M1I6M2I4M2I3M1D7M1I34M1D9M1I5M5I9M3I11M1I4M1D4M1D3M4I2M3I1M8I22M1D10M1I12M1I57M1I25M1I58M4D26M1D2M1D2M1D7M2D43M1D3M1I6M1I9M2I20M1I5M41I5M1I30M1I32M1I12M2D9M4D17M2I44M1I2M1D29M14D1M1D17M1D8M1I27M4D14M1I9M1I4M1D6M1I12M5I26M3D2M1D2M1D18M
-tctgA	50001	19011	26774	+	ctgA	49186	18755	26306	6872	8319	60	NM:i:1447	ms:i:9750	AS:i:8692	nn:i:0	tp:A:P	cm:i:376	s1:i:3010	s2:i:212	de:f:0.0832	zd:i:3	rl:i:0	cg:Z:17M1I43M1D4M7D2M7D13M2I3M1I7M1I19M1D5M1D32M1D5M2I63M4D20M5D50M2I12M1I16M3D8M1I19M2D38M1D28M7I2M1I5M4I1M1I3M2I2M1D25M1I10M1D2M1D19M1I5M1D32M1I8M5D4M8D7M1D1M1D26M2D16M2I6M7D14M4I2M1I3M2I4M1D32M6I8M1D12M1D10M1D24M4D2M1D43M1D22M1I11M1I30M2D31M1D19M1D2M1D10M3I48M1I26M4D11M1D4M1D11M2D4M1D18M7I8M1I10M1I2M1D61M1D4M1I18M1D13M3D3M2D5M8D47M1I30M3D6M1I44M2D14M1I40M9D1M2D24M1D16M39I5M1I38M3I22M4D35M1I19M1I19M1I26M1D4M1I10M4D39M1I10M2I10M1I10M1I3M1D1M5D16M1I13M1D11M1D25M1D21M8I22M4D11M1D9M5D17M1D73M1I36M6D4M1D19M1I52M1I15M24I1M1I2M2I15M1I2M6I2M1I28M1D41M4I46M4I14M1D7M21D4M1I20M1D2M1I15M1I3M1I29M1I20M5D37M2I9M1I16M1I24M1I22M3D1M2D47M1I6M1D6M1I19M1D18M1I1M1I18M1I3M1I2M1I5M35D8M1D13M1I7M4I31M1I6M1D83M2D1M1I26M1I15M1I3M2D5M2D12M1D42M1I1M2I12M4D2M4D6M26D8M3D1M1D2M4D9M1D30M2D3M2D28M1I4M1I41M1D18M1I41M1I12M1I19M4I35M5I31M4I31M1I3M1D11M1I25M2D2M3D30M1D5M1I8M1D22M1I7M1D32M1I29M6D1M7D10M3D1M1D5M1I15M7I18M2I10M4D42M1D15M1I13M1D5M1D2M2I38M1I9M2I7M3I20M1D15M1I5M1D3M1D8M2I12M1D10M1D3M1D6M1D30M1D94M1I18M1I4M5D3M1D29M1D2M1D2M1D5M1I4M1D13M1I9M6I10M1D6M1D12M2I5M2D1M1D11M2D1M1D10M5D9M8D17M1D35M1D4M1I16M5I1M1I9M8I21M23I2M1I38M1D1M1D8M1D27M1I42M1I9M2D1M1I5M1D23M2I5M1I28M1D25M1D24M1D5M1I21M1I4M4I7M1D7M1I25M21I5M1I4M1I42M2D26M1D7M1I10M1I1M1I19M10D4M1D14M1D42M8D28M3D2M3D13M1I17M1D11M1I22M1I19M1I1M4I9M2D2M1I14M8I9M2D9M1I13M2D11M3D2M2I5M1I3M1I6M3D10M1I9M1D21M1I5M2I9M2I10M1D3M2I9M1I21M3D23M1I8M1I3M1I26M1I33M8D7M1I9M10D10M1I7M1D52M10D13M1I6M2D39M1D6M1D26M1I4M1D4M32D24M1D21M2D1M1D7M1D1M1D15M1D5M1D24M2I1M1I6M1D2M1D19M35D41M3I6M3I15M2D3M1D14M2I9M3D19M2D26M1D30M1I6M3D32M1I5M1D36M1D8M1D2M2D2M1D6M3I3M7I2M2I17M1D12M1D6M1I40M3D28M2I2M2I21M1D4M1I9M1I4M1I31M2I11M1D31M1D3M2D3M5D7M4D7M1D6M1D6M8D4M1I1M2D19M3I14M1D7M1D12M1I4M3I2M4I11M1I8M1I17M1D11M1D3M1D15M17I8M3D42M1I17M1D25M1I15M1I11M2I7M1D23M4I14M2D20M1I9M3D2M1D17M1D34M1I3M1I4M1D13M1I2M1I6M1I6M1D12M2D1M4D2M4D4M1I16M36D6M1D32M1D27M1D4M1D2M1I11M20D16M3D4M1I16M1D27M1D14M1D21M2I14M1D10M3D5M2D3M3D2M1D1M4D5M1D2M3D7M1D7M1I9M1D5M1D4M1D16M1D9M9D1M1D2M1D4M1D3M2I6M2D5M1I22M1D3M1I8M1D8M3D43M1I4M1D31M1I17M3I8M2I12M6I13M1I16M1D11M2D4M1I5M2D2M2D2M1I29M1I12M2D13M1I7M14D1M1D3M5D10M1D12M5I19M1I10M1I3M7I2M14I3M9I13M2I5M1I13M1D4M1D18M1I3M1D28M1I5M4D35M1D23M3D11M2I8M1D17M1I9M1I23M4D4M1D9M1I3M1I26M1I5M3I1M1I14M1D42M1I5M16I15M1D28M4D5M1I5M1D4M1D11M2D5M1I4M1I3M1I9M
-qctgA	49186	18755	26306	+	ctgA	50001	19011	26774	6872	8319	60	NM:i:1447	ms:i:9750	AS:i:8692	nn:i:0	tp:A:P	cm:i:376	s1:i:3010	s2:i:212	de:f:0.0832	zd:i:3	rl:i:0	cg:Z:17M1D43M1I4M7I2M7I13M2D3M1D7M1D19M1I5M1I32M1I5M2D63M4I20M5I50M2D12M1D16M3I8M1D19M2I38M1I28M7D2M1D5M4D1M1D3M2D2M1I25M1D10M1I2M1I19M1D5M1I32M1D8M5I4M8I7M1I1M1I26M2I16M2D6M7I14M4D2M1D3M2D4M1I32M6D8M1I12M1I10M1I24M4I2M1I43M1I22M1D11M1D30M2I31M1I19M1I2M1I10M3D48M1D26M4I11M1I4M1I11M2I4M1I18M7D8M1D10M1D2M1I61M1I4M1D18M1I13M3I3M2I5M8I47M1D30M3I6M1D44M2I14M1D40M9I1M2I24M1I16M39D5M1D38M3D22M4I35M1D19M1D19M1D26M1I4M1D10M4I39M1D10M2D10M1D10M1D3M1I1M5I16M1D13M1I11M1I25M1I21M8D22M4I11M1I9M5I17M1I73M1D36M6I4M1I19M1D52M1D15M24D1M1D2M2D15M1D2M6D2M1D28M1I41M4D46M4D14M1I7M21I4M1D20M1I2M1D15M1D3M1D29M1D20M5I37M2D9M1D16M1D24M1D22M3I1M2I47M1D6M1I6M1D19M1I18M1D1M1D18M1D3M1D2M1D5M35I8M1I13M1D7M4D31M1D6M1I83M2I1M1D26M1D15M1D3M2I5M2I12M1I42M1D1M2D12M4I2M4I6M26I8M3I1M1I2M4I9M1I30M2I3M2I28M1D4M1D41M1I18M1D41M1D12M1D19M4D35M5D31M4D31M1D3M1I11M1D25M2I2M3I30M1I5M1D8M1I22M1D7M1I32M1D29M6I1M7I10M3I1M1I5M1D15M7D18M2D10M4I42M1I15M1D13M1I5M1I2M2D38M1D9M2D7M3D20M1I15M1D5M1I3M1I8M2D12M1I10M1I3M1I6M1I30M1I94M1D18M1D4M5I3M1I29M1I2M1I2M1I5M1D4M1I13M1D9M6D10M1I6M1I12M2D5M2I1M1I11M2I1M1I10M5I9M8I17M1I35M1I4M1D16M5D1M1D9M8D21M23D2M1D38M1I1M1I8M1I27M1D42M1D9M2I1M1D5M1I23M2D5M1D28M1I25M1I24M1I5M1D21M1D4M4D7M1I7M1D25M21D5M1D4M1D42M2I26M1I7M1D10M1D1M1D19M10I4M1I14M1I42M8I28M3I2M3I13M1D17M1I11M1D22M1D19M1D1M4D9M2I2M1D14M8D9M2I9M1D13M2I11M3I2M2D5M1D3M1D6M3I10M1D9M1I21M1D5M2D9M2D10M1I3M2D9M1D21M3I23M1D8M1D3M1D26M1D33M8I7M1D9M10I10M1D7M1I52M10I13M1D6M2I39M1I6M1I26M1D4M1I4M32I24M1I21M2I1M1I7M1I1M1I15M1I5M1I24M2D1M1D6M1I2M1I19M35I41M3D6M3D15M2I3M1I14M2D9M3I19M2I26M1I30M1D6M3I32M1D5M1I36M1I8M1I2M2I2M1I6M3D3M7D2M2D17M1I12M1I6M1D40M3I28M2D2M2D21M1I4M1D9M1D4M1D31M2D11M1I31M1I3M2I3M5I7M4I7M1I6M1I6M8I4M1D1M2I19M3D14M1I7M1I12M1D4M3D2M4D11M1D8M1D17M1I11M1I3M1I15M17D8M3I42M1D17M1I25M1D15M1D11M2D7M1I23M4D14M2I20M1D9M3I2M1I17M1I34M1D3M1D4M1I13M1D2M1D6M1D6M1I12M2I1M4I2M4I4M1D16M36I6M1I32M1I27M1I4M1I2M1D11M20I16M3I4M1D16M1I27M1I14M1I21M2D14M1I10M3I5M2I3M3I2M1I1M4I5M1I2M3I7M1I7M1D9M1I5M1I4M1I16M1I9M9I1M1I2M1I4M1I3M2D6M2I5M1D22M1I3M1D8M1I8M3I43M1D4M1I31M1D17M3D8M2D12M6D13M1D16M1I11M2I4M1D5M2I2M2I2M1D29M1D12M2I13M1D7M14I1M1I3M5I10M1I12M5D19M1D10M1D3M7D2M14D3M9D13M2D5M1D13M1I4M1I18M1D3M1I28M1D5M4I35M1I23M3I11M2D8M1I17M1D9M1D23M4I4M1I9M1D3M1D26M1D5M3D1M1D14M1I42M1D5M16D15M1I28M4I5M1D5M1I4M1I11M2I5M1D4M1D3M1D9M
-tctgA	50001	16650	18559	+	ctgA	49186	16409	18309	1708	2080	60	NM:i:372	ms:i:2437	AS:i:2143	nn:i:0	tp:A:P	cm:i:95	s1:i:761	s2:i:212	de:f:0.0792	zd:i:3	rl:i:0	cg:Z:19M5D3M3I13M1D9M1D5M2I5M8D39M1I36M2D33M1D22M1D10M2I8M1D5M1D16M6D5M2D11M2I12M1I7M1I3M3I3M1D3M1I13M1D21M1I4M2I1M1D14M1I12M1I2M1D12M6I5M1D19M10D28M1D26M1D41M1I11M1D9M1I9M4D15M6D13M1D25M5D3M1I27M2D7M1D17M7D18M2I16M1I12M1D22M2I5M12D5M7D2M1D13M1I13M2D2M1I15M1I19M1D17M1I58M1I8M11I8M1I6M2D6M1D2M1I8M2D4M15D6M1D1M2I8M3I25M1D21M1I43M1I6M1D12M2I10M14I5M1D19M3D4M1I95M2D16M2I9M3I8M1I3M1D3M4D1M1D5M3D14M1I7M1I6M2I40M1I1M2I5M1D5M1I11M7D25M10I16M1I2M2D21M1D4M1D4M1D15M2D3M1I13M13I28M2D5M1I33M1I11M1D36M1D19M1I22M1D18M1I1M1I12M1D6M9D11M2D4M1I5M10D16M5I21M1D5M1I11M37I13M3I4M1D9M1I3M1I12M1I58M1D14M
 qctgA	49186	16409	18309	+	ctgA	50001	16650	18559	1708	2080	60	NM:i:372	ms:i:2437	AS:i:2143	nn:i:0	tp:A:P	cm:i:95	s1:i:761	s2:i:212	de:f:0.0792	zd:i:3	rl:i:0	cg:Z:19M5I3M3D13M1I9M1I5M2D5M8I39M1D36M2I33M1I22M1I10M2D8M1I5M1I16M6I5M2I11M2D12M1D7M1D3M3D3M1I3M1D13M1I21M1D4M2D1M1I14M1D12M1D2M1I12M6D5M1I19M10I28M1I26M1I41M1D11M1I9M1D9M4I15M6I13M1I25M5I3M1D27M2I7M1I17M7I18M2D16M1D12M1I22M2D5M12I5M7I2M1I13M1D13M2I2M1D15M1D19M1I17M1D58M1D8M11D8M1D6M2I6M1I2M1D8M2I4M15I6M1I1M2D8M3D25M1I21M1D43M1D6M1I12M2D10M14D5M1I19M3I4M1D95M2I16M2D9M3D8M1D3M1I3M4I1M1I5M3I14M1D7M1D6M2D40M1D1M2D5M1I5M1D11M7I25M10D16M1D2M2I21M1I4M1I4M1I15M2I3M1D13M13D28M2I5M1D33M1D11M1I36M1I19M1D22M1I18M1D1M1D12M1I6M9I11M2I4M1D5M10I16M5D21M1I5M1D11M37D13M3D4M1I9M1D3M1D12M1D58M1I14M
-tctgA	50001	0	1859	+	ctgA	49186	3	1851	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1I16M1I5M3I33M1D14M3D7M1D25M2I5M2I4M1D17M3D11M1D5M3D3M1I15M3I1M2I6M1I2M6D6M2D24M1I3M2D29M1I2M1I3M1I6M1I10M2D8M19D33M1D23M2D9M1D11M1I6M1D5M1D28M1I13M1D5M1I2M1I49M5D6M2I21M1D1M2D2M2D4M4I4M1I5M1I3M1D2M1I4M37D17M2I16M6D5M3D3M6D16M5I4M8I5M4I1M1I52M2D2M1I5M28D33M1D17M2I2M2D31M42I5M1I9M1I7M1D8M1I40M1I39M1I2M1D3M2I11M2I6M2I10M1D14M1I12M1I16M1D6M3I6M2I4M1I1M1I27M1I3M10I3M2D11M3D3M1I35M1I1M3D3M2D19M3D9M4D23M1I3M1I28M1I52M1I28M1D20M2I66M1I3M2I7M1D7M2D9M1D11M1D11M1D7M1I3M1I30M1D11M1D15M2I7M3D3M1I12M6I35M1D4M1D17M1D15M1I5M1D4M1I5M1I3M5D10M1D2M1D8M7I13M5I9M1D4M1I45M6I4M1I19M2D16M1D1M2I23M7I11M1I19M1D13M
-qctgA	49186	3	1851	+	ctgA	50001	0	1859	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1D16M1D5M3D33M1I14M3I7M1I25M2D5M2D4M1I17M3I11M1I5M3I3M1D15M3D1M2D6M1D2M6I6M2I24M1D3M2I29M1D2M1D3M1D6M1D10M2I8M19I33M1I23M2I9M1I11M1D6M1I5M1I28M1D13M1I5M1D2M1D49M5I6M2D21M1I1M2I2M2I4M4D4M1D5M1D3M1I2M1D4M37I17M2D16M6I5M3I3M6I16M5D4M8D5M4D1M1D52M2I2M1D5M28I33M1I17M2D2M2I31M42D5M1D9M1D7M1I8M1D40M1D39M1D2M1I3M2D11M2D6M2D10M1I14M1D12M1D16M1I6M3D6M2D4M1D1M1D27M1D3M10D3M2I11M3I3M1D35M1D1M3I3M2I19M3I9M4I23M1D3M1D28M1D52M1D28M1I20M2D66M1D3M2D7M1I7M2I9M1I11M1I11M1I7M1D3M1D30M1I11M1I15M2D7M3I3M1D12M6D35M1I4M1I17M1I15M1D5M1I4M1D5M1D3M5I10M1I2M1I8M7D13M5D9M1I4M1D45M6D4M1D19M2I16M1I1M2D23M7D11M1D19M1I13M
-tctgA	50001	18559	19001	-	ctgA	49186	18309	18754	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:5M1I15M2I30M1D20M1D13M2D2M1D14M8I11M1D18M1I7M1I56M1D33M1D52M2D7M1I19M7D26M1I9M2I10M1I27M1D18M1I15M2I17M
 qctgA	49186	18309	18754	-	ctgA	50001	18559	19001	421	463	60	NM:i:42	ms:i:690	AS:i:668	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0539	rl:i:0	cg:Z:17M2D15M1D18M1I27M1D10M2D9M1D26M7I19M1D7M2I52M1I33M1I56M1D7M1D18M1I11M8D14M1I2M2I13M1I20M1I30M2D15M1D5M
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 tctgA	50001	1859	2192	-	ctgA	49186	1860	2214	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:14M1D4M1D3M1D9M1I12M5D20M2I43M1I10M1I7M2D2M1D8M1I30M1I9M1I2M1I6M15I39M2I16M4I2M1I35M1I2M1I6M1D42M
-qctgA	49186	1860	2214	-	ctgA	50001	1859	2192	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
+tctgA	50001	2212	16198	+	ctgA	49186	2214	15925	12504	15030	60	NM:i:2526	ms:i:17647	AS:i:15934	nn:i:0	tp:A:P	cm:i:637	s1:i:5099	s2:i:212	de:f:0.0837	zd:i:3	rl:i:0	cg:Z:10M1I4M2I21M1I10M1I14M1I5M1D29M2D9M1I15M1I27M1I12M1D5M1I11M1D7M2I4M2D9M1D4M6D32M1D13M1I55M1I8M1I1M1I12M1I2M1D22M2I56M1D11M1I5M5I17M3I3M1I13M1D16M1I50M1I2M1I10M1D1M1D42M1D2M2D33M22I3M1I2M1I6M1D8M2D5M1D50M1D6M3D6M2D12M3I13M1D9M5D1M1D10M1I3M1D5M1I3M1I4M1I24M1I5M2D30M1D3M1I15M1D9M1I3M1I18M1I9M1D11M2D6M1I23M4D1M1D22M1I3M1I11M2D1M1D7M1D4M1D18M1I6M1I5M2D5M1I66M2I3M1D8M1I13M1I8M1I3M2D4M1D20M1I5M2I22M1I6M8I14M1I6M1D8M2D5M9D7M2I4M1D11M1I20M2D2M1I33M8I10M2I7M1I18M4I5M1D4M4D1M1D33M3I10M1D20M2D8M1D9M1I10M1D7M1I8M1D6M2I66M1I3M2I2M1I24M1D63M1I14M8I7M1I13M1D31M1I16M4D41M1D3M1D4M23I9M1D2M1D8M1I1M1I12M1I2M1I3M1D33M1I24M2I3M1I4M1I12M122D6M4D2M1D13M1I3M1D35M1I4M1I13M1D32M1D6M1I5M1I5M1D12M1D8M1D48M1I2M1D19M1D9M1I24M1D13M1D8M1I5M7I5M2D10M1I11M3I15M1I6M2I4M1I18M1D14M1D3M1D1M2D17M1D12M4D15M1I3M1D31M1D1M1D1M1D1M1D12M5I2M1D31M2I18M1D5M20D10M1I20M3D11M1I14M1I1M9I4M4I2M4I2M3I4M1D10M1D50M1I14M1I11M8I11M2D9M1I20M3I5M1I27M1D5M3I9M2I9M3D34M1I21M1D15M1I9M1I2M1I2M1I8M1I26M3D4M1D3M1I2M1I25M1I1M1I14M6I45M2I21M1I17M2D23M1D6M2I8M2D20M1I24M1D9M1I1M2D6M1D3M1D9M8I4M2I30M2D8M1D7M1I50M1I3M3I26M3D17M1D17M1D5M1D8M1I29M2D2M1I3M1I6M1D11M3I20M3I19M1I17M2I33M1D35M2D7M2D3M18D1M3D10M5D11M1D8M1D6M1I9M1I4M2D5M1D13M1D22M1D16M14I22M1D3M1I19M1D53M1I13M1I20M8I8M1I6M6D28M3D28M9D23M5D26M1I6M1D5M1D24M1I5M2I13M1I2M4I2M1I4M4I8M1I14M1I12M1I28M1I18M4I10M2D8M1I62M1I14M2I5M1I18M1D1M3I4M1I13M1D4M2I3M1D8M4D2M8D71M1I8M4I23M1I15M5D13M1D6M1D8M7I16M2I13M2D27M1D46M1I20M2D6M1I9M1D4M1I7M1D6M1I2M6I11M4D25M1I22M1D14M2D20M1D30M3I7M3D4M1I22M1D4M1D10M1D20M1I21M3I3M1I8M1D14M1I10M2I45M1D14M1D17M1D27M2D3M1I2M2I4M1D13M1D5M4I6M2I11M1I11M4I6M1I15M1I8M1I6M9I1M1I19M1I4M1I8M2D9M1I7M1D33M1D19M1D3M1D35M3D4M1D6M2D16M3D1M1D30M26D28M1D7M2I12M2D10M1I7M1D16M1D4M1I18M1I33M1I31M1I7M1I12M1D7M1D16M5I3M1I4M1D4M1D28M8D12M1D4M1D7M3D11M1D15M1D12M1I12M3I6M2D4M1D16M1I11M1D5M1D2M2I22M4D14M2I19M1D7M3I17M1I22M5D6M1D14M2D1M1D12M1I11M10I16M1D21M1D24M5D17M1D48M1D3M1D4M1D12M1D13M4D9M1I22M1I21M1I12M1D11M3D2M1D9M1I10M1D4M1I4M1D18M1I3M1D18M2D4M1I21M4D5M3I3M1D21M1I33M1D19M1I38M2I27M1I7M1I15M2I8M5D2M1D15M1I7M2I2M1I11M1D24M1I4M1D14M1I51M1D47M1D3M4D4M3D3M1I3M1D13M1D3M1I13M1I10M3I34M1D3M1I17M1D5M1I8M1D28M1I13M2I2M1I16M1D21M2I22M5I8M1I3M1I9M1D12M2D11M1I7M1I2M2D10M3I26M4D12M1D3M1D12M7I12M1I5M1D5M8D5M1D8M1I31M1D3M1D6M1I12M2D4M1D24M2I10M1I17M1D1M3D11M1D8M2D16M1D18M2D3M6D2M1D6M24D10M2I14M1I11M1I4M1D10M1I34M4I14M1D21M1D6M43D8M4D2M1D12M1D7M5D4M2I15M1D39M1D6M1I9M3D1M3D2M2D4M4D2M3D1M1D2M1D10M1I16M3D17M1I1M1I28M1D10M1D11M1D28M1D11M2I17M1I14M1I7M2D6M1D4M7D3M7D10M1I6M1I57M2D4M1D5M1D18M2I50M5I38M1D6M1D15M1D5M1I58M4I28M1I15M1D14M3I4M2D4M1I11M4D4M1D44M1I25M1I8M2D12M1I7M1D31M1D9M26I5M1I19M1D1M1D9M1D5M1D7M34I1M1I38M1I1M1I21M1D4M11D29M1D11M1D7M3I19M2I36M1D12M1I21M1I2M7I23M2I19M1I6M1I16M2I2M3D10M1D11M10I5M1I15M2D18M1I17M1I7M2D6M2I6M1D27M1I17M1I23M5I29M4D3M1I41M1D33M1D9M1D11M6I25M1D17M3D6M1I8M1I14M1D13M1D12M1I16M1I12M1I3M1D12M1I28M1D32M1D15M1I32M6I2M2I8M1D6M1D23M22I30M1I9M10D58M3I7M1D12M1I10M6I31M1D14M1I38M1I13M3D14M1D23M1I6M1I10M3I22M1I10M1I8M5I67M1I13M4D3M5D6M1I4M1I8M3D8M3I2M1I11M1D11M1I4M2I1M1I2M1I5M3I9M2D1M1D4M1D6M2D5M1D5M1I8M4D8M1I7M2I3M3D15M6D1M1D9M1D4M1D6M1D36M1D7M1D18M1I5M1D3M2I20M1D13M4I7M5I2M2I43M1I5M1D12M1I7M1D31M1I13M1D13M1I6M1D1M1D4M3D7M1D31M2D26M1I7M1I8M1D7M1I17M1D18M1I6M1D4M7D13M1I6M1D7M1I31M1D5M1I15M1D20M1I20M1I26M3I2M3I1M9I5M1I24M2D25M1D14M1D5M3D2M1I7M1I3M1I19M1I17M1I16M2I5M5D8M1I15M1I3M2I5M5I15M1D13M3D7M1D9M5I10M2D5M1I10M2I1M1I2M1I9M8I2M1D5M1I6M6D7M1I13M3I7M1I3M1D15M2D18M1D3M1D2M1D5M1D5M2I9M1I1M1I27M1I11M1D16M8I1M2I8M1I15M1I6M1I10M1D24M1D3M1D19M1I12M1I24M1D8M1D2M1D2M1I6M1D31M2I5M5D16M5I5M1I6M3D11M14D12M3I29M1I12M1I5M23I2M1I4M4I6M1D41M2I21M1D17M1D5M1D25M3I18M1D6M1D5M1D42M1I3M1D31M1I3M1D14M1D21M1I8M3D4M1I19M6D10M2I12M7I32M8I2M1D18M2D31M1D15M1I21M1I6M1I3M1I39M2I1M1D10M1D3M1I36M12D45M1D7M1I4M1I1M3I7M1I3M1D5M1D6M1D14M1D14M1I18M1D1M1D6M1I1M2D1M1D4M2D8M1D27M5I20M12D11M1D9M1D29M3D26M2D4M2D3M1I6M37D1M1D4M5D3M1D3M6D3M4D16M1D27M2D3M1D2M2D60M4D5M4I8M21D26M1D16M1D3M1I8M1D22M1I8M10D3M2D3M3D13M36D4M1D40M1I6M1I5M1I7M2I7M1I13M2I2M1D8M2I6M1I9M1I3M1D4M4I3M1D5M1I11M1D4M4D23M1I21M1I17M1D37M2I10M1D36M1D8M1D1M1D9M1I6M1D1M5D1M7D3M2D2M10D2M2D12M1I27M2I1M1D16M1D18M1D25M1D29M1I12M2I18M1I2M3I3M7I13M1D30M3D2M2D18M1D4M2D36M1I19M1D19M1I6M1I4M3D20M2D13M1I61M1I12M3D1M1D6M2D4M2D3M1I7M1D34M1I9M1D5M5D9M3D11M1D4M1I4M1I3M4D2M3D1M8D22M1I10M1D12M1D57M1D25M1D58M4I26M1I2M1I2M1I7M2I43M1I3M1D6M1D9M2D20M1D5M41D5M1D30M1D32M1D12M2I9M4I17M2D44M1D2M1I29M14I1M1I17M1I8M1D27M4I14M1D9M1D4M1I6M1D12M5D26M3I2M1I2M1I18M
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8D30M2I15M2I13M1D6M5D5M3D17M2D17M2I18M2D11M1I11M2I3M1D18M1D9M1I8M1I16M1D2M1D13M3D1M1D10M1D11M1I8M3D3M1I26M1D4M2D8M1D3M2D4M1I4M2I11M1D10M1D4M1D8M6D1M1D5M7D2M1D5M8D3M2D13M4I1M1I17M1D21M1D22M1I10M1D41M1I2M1I2M1I5M1D41M1D29M1I5M1D5M1I8M1I15M1D9M1D22M1D29M4D7M1I9M1D8M1I32M2D15M1I15M1I23M1I7M10I19M1D38M1I7M1I4M1I16M28D29M7D28M1D52M2I6M1I1M1I1M1I3M1I25M2D15M1I9M5D6M1D12M1I6M1I4M2I11M5D1M2D1M4D15M3I11M3D4M1I8M1D40M6I12M1D17M1D9M5D1M1D2M1D25M1I23M2D9M1D11M1I3M2D28M1I12M1I17M15I10M1D9M1I2M1I8M4I11M1D9M1I6M1I8M1I40M2D3M2I8M1D11M1D16M1D6M1I7M1I34M2I27M1I5M1D3M2D39M1I30M1D22M1I10M3D61M2I19M2I6M1D7M1I23M1I4M1D3M1D6M2I12M2D11M14I13M1D6M4I9M2D11M1I17M1I4M1D8M1D3M1I4M1I35M1D47M1D17M1I7M1I2M1I25M1I13M1D3M1D18M1I13M2D10M2I19M2I6M1D6M1I7M1I11M1I6M3D2M1D11M1I6M1D17M12I1M1I2M1I9M1D1M1D7M7I4M1I9M8I12M1I37M1I25M4I1M1D7M3D13M1I4M1D2M1D43M1D11M1I4M1I6M1D31M2I38M2D12M2D6M2I39M1I19M6I1M1I12M1D16M1D50M1D40M1D24M1I4M2D5M1D5M2I13M2I4M7D2M2D2M7D1M3D15M1I8M1D10M10D41M1I34M1I10M1D11M1I3M3D7M3I23M9D47M2D19M1I36M42D2M1I3M1D3M1D7M1D5M3D6M1D16M1D13M1D39M14I7M1I16M1D19M1D14M1D8M1I34M2I3M1D6M1D12M2I3M1D10M2I1M1D6M39D2M2D16M2I3M2I3M1D23M1D14M3D3M2D6M3D2M1D1M1D10M1D25M1I17M2I33M2D2M1I7M1I36M2D13M1I9M1D6M3I11M1I2M1D8M1D21M1I34M1D12M2I3M1I8M4I11M1D59M5D18M2I11M1I4M7D26M2I77M5D11M1I16M2D6M5I19M1D13M1D1M2D23M1D6M2I11M1D35M1D10M1I14M1D30M1D12M38D2M1D3M1I2M1I5M2D7M1I1M2I3M1I57M1I31M1I9M1I63M1I40M2I3M1I25M1I4M2I21M15I10M1I30M2D3M2D6M2D15M1I6M1I48M2I27M1D6M1D77M2D3M1I22M3D20M1I14M1I29M1I16M1D20M1D5M30D25M6D7M1I17M1I5M14D16M1I3M1D15M1D41M1D13M1I13M1D5M2D19M2I6M1D29M1I2M2D16M1D6M1D8M1I4M9I13M3D10M1I16M4D27M1D1M3D6M2I9M5I38M1D3M2D1M1D4M2I5M1I24M1D18M1I3M5D2M3D3M1I3M1D1M1D5M1D4M1D11M5D3M8D6M1I3M2D5M1D11M1I19M1I1M1I15M1I3M1D15M1D5M3D1M1D12M1D23M1D1M1D6M4I2M4I9M1I17M1I4M1D18M3I7M1I51M11D11M1D12M3D17M1D14M2I12M4I10M1D26M1I45M1I3M1D15M2I11M1I28M1I4M2D9M1I31M3I15M1I11M1D3M4I10M1I21M1D31M8I23M4I24M1D13M5I19M2D1M1D5M10D10M1I23M1I20M2I32M1D5M1D23M1D9M1I14M1I22M1D6M1D19M3I14M1I18M1D10M1D7M1D14M1D46M1D7M21I5M1D17M3D2M4D7M1D16M1I2M1I14M1I3M1I4M1I16M2I42M1I7M1I17M5D1M1D29M13D24M1I3M8I5M12I9M1I23M1D8M
 "
 `;
diff --git a/products/jbrowse-cli/src/commands/create-pif.test.ts b/products/jbrowse-cli/src/commands/create-pif.test.ts
index 6de1367302..59630f979f 100644
--- a/products/jbrowse-cli/src/commands/create-pif.test.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.test.ts
@@ -5,6 +5,7 @@
 import path from 'path'
 import fs from 'fs'
 import { setup } from '../testUtil'
+import { gunzipSync } from 'zlib'
 
 const base = path.join(__dirname, '..', '..', 'test', 'data')
 const simplePaf = path.join(base, 'volvox_inv_indels.paf')
@@ -17,5 +18,6 @@ describe('create-pif', () => {
     .command(['create-pif', simplePaf, '--out', fn])
     .it('processes volvox paf', () => {
       expect(exists(fn)).toBeTruthy()
+      expect(gunzipSync(fs.readFileSync(fn)).toString()).toMatchSnapshot()
     })
 })
diff --git a/products/jbrowse-cli/src/commands/create-pif.ts b/products/jbrowse-cli/src/commands/create-pif.ts
index 7287b9e87d..e63ee543ac 100644
--- a/products/jbrowse-cli/src/commands/create-pif.ts
+++ b/products/jbrowse-cli/src/commands/create-pif.ts
@@ -47,12 +47,15 @@ export function swapIndelCigar(cigar: string) {
   return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
 }
 
-export async function createPIF(filename?: string, child: { stdin: any }) {
+export async function createPIF(
+  filename: string | undefined,
+  stream: { write: any },
+) {
   const rl1 = filename ? getReadline(filename) : getStdReadline()
   for await (const line of rl1) {
     const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t')
 
-    child.stdin.write(
+    stream.write(
       [`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n',
     )
     const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'))
@@ -66,7 +69,7 @@ export async function createPIF(filename?: string, child: { stdin: any }) {
       }`
     }
 
-    child.stdin.write(
+    stream.write(
       [`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n',
     )
   }
@@ -101,40 +104,41 @@ export default class CreatePIF extends JBrowseCommand {
   }
 
   async run() {
-    try {
-      const {
-        args: { file },
-        flags: { out, csi },
-      } = await this.parse(CreatePIF)
-
-      if (
-        commandExistsSync('sh') &&
-        commandExistsSync('sort') &&
-        commandExistsSync('grep') &&
-        commandExistsSync('tabix') &&
-        commandExistsSync('bgzip')
-      ) {
-        const fn = out || `${path.basename(file, '.paf')}.pif.gz`
-        console.error('start')
-        const child = spawn(
-          'sh',
-          [
-            '-c',
-            `sort -t"\`printf '\t'\`" -k1,1 -k3,3n ${fn} | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
-          ],
-          {
-            env: { ...process.env, LC_ALL: 'C' },
-            stdio: 'inherit',
-          },
-        )
-        await createPIF(fn, child)
-      } else {
-        throw new Error(
-          'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
-        )
-      }
-    } catch (e) {
-      console.error(e)
+    const {
+      args: { file },
+      flags: { out, csi },
+    } = await this.parse(CreatePIF)
+    console.error('wtf')
+
+    if (
+      commandExistsSync('sh') &&
+      commandExistsSync('sort') &&
+      commandExistsSync('grep') &&
+      commandExistsSync('tabix') &&
+      commandExistsSync('bgzip')
+    ) {
+      console.error('wtf')
+      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+      const child = spawn(
+        'sh',
+        [
+          '-c',
+          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+        ],
+        {
+          env: { ...process.env, LC_ALL: 'C' },
+          stdio: ['pipe', process.stdout, process.stderr],
+        },
+      )
+      await createPIF(file, child.stdin)
+      child.stdin.end()
+      await new Promise(resolve => {
+        child.on('close', resolve)
+      })
+    } else {
+      throw new Error(
+        'Unable to sort, requires unix type environment with sort, grep, bgzip, tabix',
+      )
     }
   }
 }

From 87209ca22a03fa67f53a11bda8324f6808fcdcb6 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 10:09:56 -0500
Subject: [PATCH 11/12] Create the jbrowse pif command

---
 products/jbrowse-cli/README.md                |  48 +++++++++---------
 products/jbrowse-cli/out.paf                  |   7 +++
 products/jbrowse-cli/out.pif.gz               | Bin 0 -> 295 bytes
 products/jbrowse-cli/out.pif.gz.tbi           | Bin 0 -> 169 bytes
 .../{create-pif.test.ts => make-pif.test.ts}  |   8 ++-
 .../commands/{create-pif.ts => make-pif.ts}   |  22 ++++----
 6 files changed, 48 insertions(+), 37 deletions(-)
 create mode 100644 products/jbrowse-cli/out.paf
 create mode 100644 products/jbrowse-cli/out.pif.gz
 create mode 100644 products/jbrowse-cli/out.pif.gz.tbi
 rename products/jbrowse-cli/src/commands/{create-pif.test.ts => make-pif.test.ts} (68%)
 rename products/jbrowse-cli/src/commands/{create-pif.ts => make-pif.ts} (84%)

diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
index af57958da3..f0b3dc0a74 100644
--- a/products/jbrowse-cli/README.md
+++ b/products/jbrowse-cli/README.md
@@ -53,8 +53,8 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track)
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
-- [`jbrowse create-pif FILE`](#jbrowse-create-pif-file)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
+- [`jbrowse make-pif FILE`](#jbrowse-make-pif-file)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -458,56 +458,56 @@ EXAMPLES
 _See code:
 [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse create-pif FILE`
+## `jbrowse help [COMMANDS]`
 
-creates pairwise indexed PAF (PIF), with bgzip and tabix
+Display help for jbrowse.
 
 ```
 USAGE
-  $ jbrowse create-pif FILE [--out <value>] [--csi <value>] [-h]
+  $ jbrowse help [COMMANDS] [-n]
 
 ARGUMENTS
-  FILE  PAF file as input
+  COMMANDS  Command to show help for.
 
 FLAGS
-  -h, --help         Show CLI help.
-      --csi=<value>  Create a CSI index for the PIF file instead of TBI
-      --out=<value>  Where to write the output file. If unspecified, will be ${file}.pif.gz
+  -n, --nested-commands  Include all nested commands in the output.
 
 DESCRIPTION
-  creates pairwise indexed PAF (PIF), with bgzip and tabix
-
-EXAMPLES
-  $ jbrowse create-pif input.paf # creates input.pif.gz in same directory
-
-
-
-  $ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+  Display help for jbrowse.
 ```
 
 _See code:
-[src/commands/create-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pif.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
-## `jbrowse help [COMMANDS]`
+## `jbrowse make-pif FILE`
 
-Display help for jbrowse.
+creates pairwise indexed PAF (PIF), with bgzip and tabix
 
 ```
 USAGE
-  $ jbrowse help [COMMANDS] [-n]
+  $ jbrowse make-pif FILE [--out <value>] [--csi] [-h]
 
 ARGUMENTS
-  COMMANDS  Command to show help for.
+  FILE  PAF file as input
 
 FLAGS
-  -n, --nested-commands  Include all nested commands in the output.
+  -h, --help         Show CLI help.
+      --csi          Create a CSI index for the PIF file instead of TBI
+      --out=<value>  Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi
 
 DESCRIPTION
-  Display help for jbrowse.
+  creates pairwise indexed PAF (PIF), with bgzip and tabix
+
+EXAMPLES
+  $ jbrowse pif input.paf # creates input.pif.gz in same directory
+
+
+
+  $ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
diff --git a/products/jbrowse-cli/out.paf b/products/jbrowse-cli/out.paf
new file mode 100644
index 0000000000..56c2b2cbe8
--- /dev/null
+++ b/products/jbrowse-cli/out.paf
@@ -0,0 +1,7 @@
+ctgA	45141	1	45141	+	ctgA	50001	1	50001	45135	50000	60	tp:A:P	cm:i:8494	s1:i:44546	s2:i:0	dv:f:0	rl:i:0
+ctgB	6079	2	6079	+	ctgB	6079	2	6079	6077	6077	2	tp:A:P	cm:i:1213	s1:i:6077	s2:i:6027	dv:f:0	rl:i:0
+ctgB	6079	52	6079	+	ctgB	6079	2	6029	6027	6027	0	tp:A:S	cm:i:1203	s1:i:6027	dv:f:0.0001	rl:i:0
+ctgB	6079	2	6029	+	ctgB	6079	52	6079	6027	6027	0	tp:A:S	cm:i:1203	s1:i:6027	dv:f:0	rl:i:0
+ctgB	6079	102	6079	+	ctgB	6079	2	5979	5977	5977	0	tp:A:S	cm:i:1193	s1:i:5977	dv:f:0.0001	rl:i:0
+ctgB	6079	2	5979	+	ctgB	6079	102	6079	5977	5977	0	tp:A:S	cm:i:1193	s1:i:5977	dv:f:0	rl:i:0
+ctgB	6079	2	5929	+	ctgB	6079	152	6079	5927	5927	0	tp:A:S	cm:i:1183	s1:i:5927	dv:f:0	rl:i:0
diff --git a/products/jbrowse-cli/out.pif.gz b/products/jbrowse-cli/out.pif.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d191af2e6a06222b93757c3d2bdd3e6753387390
GIT binary patch
literal 295
zcmb2|=3rp}f&Xj_PR>jWT#Q?%-0fmA<Y`_1cs0kQD`iR5%l#F8aCB|j&}5%Fzdkvb
zJNS5$)x9M%TYmbf6~CyI=J(#vr^EQPm}}(=fsbKVf}@J37q##y&O2nZCb62wJ~44`
ztF~v_+Rd^ty-PTD@82-}@u%wQS#w%<PBOpQ%=o-Fd}fSNy2(Vo>=RPbR~4epgesfP
z&RKUO;>H=NtZn)^d7G@)Jlof=%X=+gA#Ykqmf6LtH(JlEIrwFoUmI8Ctjy=Ryx(1p
z?6LT#^Yh`v_-}W_J^nvldi6WYqXzNKj=$Iay|UmVw_4SYNfYN@c~pPYudv3NcY%BH
jC4uUScO}YuOMm`hc8)hubz)^;kVgv&X$EF+$bbj{Wd(oc

literal 0
HcmV?d00001

diff --git a/products/jbrowse-cli/out.pif.gz.tbi b/products/jbrowse-cli/out.pif.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..f4afa1cf54a7afdbd61fbbd6f244c1a14fc38cb5
GIT binary patch
literal 169
zcmb2|=3rp}f&Xj_PR>jWJq+B1pHfm18yMUa(%6y&;w81z7>~4`RDIc(aH(@4%Nae!
z%`+Q{=J^QJ8cg6^x>wDx;pxSr6R#RMygkf%;2F2$mjhq)Q=ClYW9RUm<w@Cl;$7>?
z=Sgm+{IN23_v(0L6<j>=?pagygxP{O<w^>3-aT{TmSM<_u`6A}$iN_v<``)PX0Y2p
F1OU4`J4gTk

literal 0
HcmV?d00001

diff --git a/products/jbrowse-cli/src/commands/create-pif.test.ts b/products/jbrowse-cli/src/commands/make-pif.test.ts
similarity index 68%
rename from products/jbrowse-cli/src/commands/create-pif.test.ts
rename to products/jbrowse-cli/src/commands/make-pif.test.ts
index 59630f979f..3f2cce0a0f 100644
--- a/products/jbrowse-cli/src/commands/create-pif.test.ts
+++ b/products/jbrowse-cli/src/commands/make-pif.test.ts
@@ -12,12 +12,16 @@ const simplePaf = path.join(base, 'volvox_inv_indels.paf')
 
 const exists = (p: string) => fs.existsSync(p)
 
-describe('create-pif', () => {
+describe('make-pif', () => {
   const fn = path.basename(simplePaf, '.paf') + '.pif.gz'
   setup
-    .command(['create-pif', simplePaf, '--out', fn])
+    .command(['make-pif', simplePaf, '--out', fn])
     .it('processes volvox paf', () => {
       expect(exists(fn)).toBeTruthy()
       expect(gunzipSync(fs.readFileSync(fn)).toString()).toMatchSnapshot()
     })
+  setup.command(['make-pif', simplePaf, '--out', fn, '--csi']).it('csi', () => {
+    expect(exists(fn)).toBeTruthy()
+    expect(exists(fn + '.csi')).toBeTruthy()
+  })
 })
diff --git a/products/jbrowse-cli/src/commands/create-pif.ts b/products/jbrowse-cli/src/commands/make-pif.ts
similarity index 84%
rename from products/jbrowse-cli/src/commands/create-pif.ts
rename to products/jbrowse-cli/src/commands/make-pif.ts
index e63ee543ac..77a4719bf4 100644
--- a/products/jbrowse-cli/src/commands/create-pif.ts
+++ b/products/jbrowse-cli/src/commands/make-pif.ts
@@ -49,7 +49,7 @@ export function swapIndelCigar(cigar: string) {
 
 export async function createPIF(
   filename: string | undefined,
-  stream: { write: any },
+  stream: { write: (arg: string) => void },
 ) {
   const rl1 = filename ? getReadline(filename) : getStdReadline()
   for await (const line of rl1) {
@@ -76,22 +76,22 @@ export async function createPIF(
   rl1.close()
 }
 
-export default class CreatePIF extends JBrowseCommand {
+export default class MakePIF extends JBrowseCommand {
   static description =
     'creates pairwise indexed PAF (PIF), with bgzip and tabix'
 
   static examples = [
-    '$ jbrowse create-pif input.paf # creates input.pif.gz in same directory',
+    '$ jbrowse pif input.paf # creates input.pif.gz in same directory',
     '',
-    '$ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
+    '$ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
   ]
 
   static flags = {
     out: Flags.string({
       description:
-        'Where to write the output file. If unspecified, will be ${file}.pif.gz',
+        'Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi',
     }),
-    csi: Flags.string({
+    csi: Flags.boolean({
       description: 'Create a CSI index for the PIF file instead of TBI',
     }),
     help: Flags.help({ char: 'h' }),
@@ -107,8 +107,7 @@ export default class CreatePIF extends JBrowseCommand {
     const {
       args: { file },
       flags: { out, csi },
-    } = await this.parse(CreatePIF)
-    console.error('wtf')
+    } = await this.parse(MakePIF)
 
     if (
       commandExistsSync('sh') &&
@@ -117,13 +116,14 @@ export default class CreatePIF extends JBrowseCommand {
       commandExistsSync('tabix') &&
       commandExistsSync('bgzip')
     ) {
-      console.error('wtf')
-      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+      const fn = out || `${path.basename(file || 'output', '.paf')}.pif.gz`
       const child = spawn(
         'sh',
         [
           '-c',
-          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix ${
+            csi ? '-C ' : ''
+          }-s1 -b3 -e4 ${fn}`,
         ],
         {
           env: { ...process.env, LC_ALL: 'C' },

From 31d04e5b8bc1418c929c1210e82587b6f80ff45e Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 11 Dec 2023 10:59:12 -0500
Subject: [PATCH 12/12] Add bgzip and tabix to testing

---
 .github/workflows/push.yml                                   | 5 +++--
 .github/workflows/website.yml                                | 2 +-
 .../{create-pif.test.ts.snap => make-pif.test.ts.snap}       | 2 +-
 3 files changed, 5 insertions(+), 4 deletions(-)
 rename products/jbrowse-cli/src/commands/__snapshots__/{create-pif.test.ts.snap => make-pif.test.ts.snap} (99%)

diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
index 7b0aa3d5c5..ed12da25f7 100644
--- a/.github/workflows/push.yml
+++ b/.github/workflows/push.yml
@@ -7,11 +7,12 @@ jobs:
     name: Test and typecheck on node 20.x and ubuntu-latest
     runs-on: ubuntu-latest
     steps:
+      - run: sudo apt-get -y install tabix
       - uses: actions/checkout@v4
       - name: Use Node.js 20.x
         uses: actions/setup-node@v4
         with:
-          node-version: '20.5.1'
+          node-version: '20'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Test codebase
@@ -29,7 +30,7 @@ jobs:
       - name: Use Node.js 20
         uses: actions/setup-node@v4
         with:
-          node-version: '20.5.1'
+          node-version: '20'
       - name: Install website deps (with cache)
         uses: bahmutov/npm-install@v1
         with:
diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index 5c26ce5fb1..a6c917e8f8 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -13,7 +13,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4
         with:
-          node-version: '20.5.1'
+          node-version: '20'
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v2
         with:
diff --git a/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/make-pif.test.ts.snap
similarity index 99%
rename from products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
rename to products/jbrowse-cli/src/commands/__snapshots__/make-pif.test.ts.snap
index da66ddcf40..4f8b5d1696 100644
--- a/products/jbrowse-cli/src/commands/__snapshots__/create-pif.test.ts.snap
+++ b/products/jbrowse-cli/src/commands/__snapshots__/make-pif.test.ts.snap
@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`create-pif processes volvox paf 1`] = `
+exports[`make-pif processes volvox paf 1`] = `
 "qctgA	49186	3	1851	+	ctgA	50001	0	1859	1633	2044	60	NM:i:411	ms:i:2207	AS:i:1899	nn:i:0	tp:A:P	cm:i:87	s1:i:696	s2:i:212	de:f:0.0908	zd:i:1	rl:i:0	cg:Z:4M1D16M1D5M3D33M1I14M3I7M1I25M2D5M2D4M1I17M3I11M1I5M3I3M1D15M3D1M2D6M1D2M6I6M2I24M1D3M2I29M1D2M1D3M1D6M1D10M2I8M19I33M1I23M2I9M1I11M1D6M1I5M1I28M1D13M1I5M1D2M1D49M5I6M2D21M1I1M2I2M2I4M4D4M1D5M1D3M1I2M1D4M37I17M2D16M6I5M3I3M6I16M5D4M8D5M4D1M1D52M2I2M1D5M28I33M1I17M2D2M2I31M42D5M1D9M1D7M1I8M1D40M1D39M1D2M1I3M2D11M2D6M2D10M1I14M1D12M1D16M1I6M3D6M2D4M1D1M1D27M1D3M10D3M2I11M3I3M1D35M1D1M3I3M2I19M3I9M4I23M1D3M1D28M1D52M1D28M1I20M2D66M1D3M2D7M1I7M2I9M1I11M1I11M1I7M1D3M1D30M1I11M1I15M2D7M3I3M1D12M6D35M1I4M1I17M1I15M1D5M1I4M1D5M1D3M5I10M1I2M1I8M7D13M5D9M1I4M1D45M6D4M1D19M2I16M1I1M2D23M7D11M1D19M1I13M
 qctgA	49186	1860	2214	-	ctgA	50001	1859	2192	321	366	60	NM:i:45	ms:i:501	AS:i:468	nn:i:0	tp:A:I	cm:i:0	s1:i:0	s2:i:0	de:f:0.0614	rl:i:0	cg:Z:42M1I6M1D2M1D35M1D2M4D16M2D39M15D6M1D2M1D9M1D30M1D8M1I2M2I7M1D10M1D43M2D20M5I12M1D9M1I3M1I4M1I14M
 qctgA	49186	2214	15925	+	ctgA	50001	2212	16198	12504	15030	60	NM:i:2526	ms:i:17647	AS:i:15934	nn:i:0	tp:A:P	cm:i:637	s1:i:5099	s2:i:212	de:f:0.0837	zd:i:3	rl:i:0	cg:Z:10M1D4M2D21M1D10M1D14M1D5M1I29M2I9M1D15M1D27M1D12M1I5M1D11M1I7M2D4M2I9M1I4M6I32M1I13M1D55M1D8M1D1M1D12M1D2M1I22M2D56M1I11M1D5M5D17M3D3M1D13M1I16M1D50M1D2M1D10M1I1M1I42M1I2M2I33M22D3M1D2M1D6M1I8M2I5M1I50M1I6M3I6M2I12M3D13M1I9M5I1M1I10M1D3M1I5M1D3M1D4M1D24M1D5M2I30M1I3M1D15M1I9M1D3M1D18M1D9M1I11M2I6M1D23M4I1M1I22M1D3M1D11M2I1M1I7M1I4M1I18M1D6M1D5M2I5M1D66M2D3M1I8M1D13M1D8M1D3M2I4M1I20M1D5M2D22M1D6M8D14M1D6M1I8M2I5M9I7M2D4M1I11M1D20M2I2M1D33M8D10M2D7M1D18M4D5M1I4M4I1M1I33M3D10M1I20M2I8M1I9M1D10M1I7M1D8M1I6M2D66M1D3M2D2M1D24M1I63M1D14M8D7M1D13M1I31M1D16M4I41M1I3M1I4M23D9M1I2M1I8M1D1M1D12M1D2M1D3M1I33M1D24M2D3M1D4M1D12M122I6M4I2M1I13M1D3M1I35M1D4M1D13M1I32M1I6M1D5M1D5M1I12M1I8M1I48M1D2M1I19M1I9M1D24M1I13M1I8M1D5M7D5M2I10M1D11M3D15M1D6M2D4M1D18M1I14M1I3M1I1M2I17M1I12M4I15M1D3M1I31M1I1M1I1M1I1M1I12M5D2M1I31M2D18M1I5M20I10M1D20M3I11M1D14M1D1M9D4M4D2M4D2M3D4M1I10M1I50M1D14M1D11M8D11M2I9M1D20M3D5M1D27M1I5M3D9M2D9M3I34M1D21M1I15M1D9M1D2M1D2M1D8M1D26M3I4M1I3M1D2M1D25M1D1M1D14M6D45M2D21M1D17M2I23M1I6M2D8M2I20M1D24M1I9M1D1M2I6M1I3M1I9M8D4M2D30M2I8M1I7M1D50M1D3M3D26M3I17M1I17M1I5M1I8M1D29M2I2M1D3M1D6M1I11M3D20M3D19M1D17M2D33M1I35M2I7M2I3M18I1M3I10M5I11M1I8M1I6M1D9M1D4M2I5M1I13M1I22M1I16M14D22M1I3M1D19M1I53M1D13M1D20M8D8M1D6M6I28M3I28M9I23M5I26M1D6M1I5M1I24M1D5M2D13M1D2M4D2M1D4M4D8M1D14M1D12M1D28M1D18M4D10M2I8M1D62M1D14M2D5M1D18M1I1M3D4M1D13M1I4M2D3M1I8M4I2M8I71M1D8M4D23M1D15M5I13M1I6M1I8M7D16M2D13M2I27M1I46M1D20M2I6M1D9M1I4M1D7M1I6M1D2M6D11M4I25M1D22M1I14M2I20M1I30M3D7M3I4M1D22M1I4M1I10M1I20M1D21M3D3M1D8M1I14M1D10M2D45M1I14M1I17M1I27M2I3M1D2M2D4M1I13M1I5M4D6M2D11M1D11M4D6M1D15M1D8M1D6M9D1M1D19M1D4M1D8M2I9M1D7M1I33M1I19M1I3M1I35M3I4M1I6M2I16M3I1M1I30M26I28M1I7M2D12M2I10M1D7M1I16M1I4M1D18M1D33M1D31M1D7M1D12M1I7M1I16M5D3M1D4M1I4M1I28M8I12M1I4M1I7M3I11M1I15M1I12M1D12M3D6M2I4M1I16M1D11M1I5M1I2M2D22M4I14M2D19M1I7M3D17M1D22M5I6M1I14M2I1M1I12M1D11M10D16M1I21M1I24M5I17M1I48M1I3M1I4M1I12M1I13M4I9M1D22M1D21M1D12M1I11M3I2M1I9M1D10M1I4M1D4M1I18M1D3M1I18M2I4M1D21M4I5M3D3M1I21M1D33M1I19M1D38M2D27M1D7M1D15M2D8M5I2M1I15M1D7M2D2M1D11M1I24M1D4M1I14M1D51M1I47M1I3M4I4M3I3M1D3M1I13M1I3M1D13M1D10M3D34M1I3M1D17M1I5M1D8M1I28M1D13M2D2M1D16M1I21M2D22M5D8M1D3M1D9M1I12M2I11M1D7M1D2M2I10M3D26M4I12M1I3M1I12M7D12M1D5M1I5M8I5M1I8M1D31M1I3M1I6M1D12M2I4M1I24M2D10M1D17M1I1M3I11M1I8M2I16M1I18M2I3M6I2M1I6M24I10M2D14M1D11M1D4M1I10M1D34M4D14M1I21M1I6M43I8M4I2M1I12M1I7M5I4M2D15M1I39M1I6M1D9M3I1M3I2M2I4M4I2M3I1M1I2M1I10M1D16M3I17M1D1M1D28M1I10M1I11M1I28M1I11M2D17M1D14M1D7M2I6M1I4M7I3M7I10M1D6M1D57M2I4M1I5M1I18M2D50M5D38M1I6M1I15M1I5M1D58M4D28M1D15M1I14M3D4M2I4M1D11M4I4M1I44M1D25M1D8M2I12M1D7M1I31M1I9M26D5M1D19M1I1M1I9M1I5M1I7M34D1M1D38M1D1M1D21M1I4M11I29M1I11M1I7M3D19M2D36M1I12M1D21M1D2M7D23M2D19M1D6M1D16M2D2M3I10M1I11M10D5M1D15M2I18M1D17M1D7M2I6M2D6M1I27M1D17M1D23M5D29M4I3M1D41M1I33M1I9M1I11M6D25M1I17M3I6M1D8M1D14M1I13M1I12M1D16M1D12M1D3M1I12M1D28M1I32M1I15M1D32M6D2M2D8M1I6M1I23M22D30M1D9M10I58M3D7M1I12M1D10M6D31M1I14M1D38M1D13M3I14M1I23M1D6M1D10M3D22M1D10M1D8M5D67M1D13M4I3M5I6M1D4M1D8M3I8M3D2M1D11M1I11M1D4M2D1M1D2M1D5M3D9M2I1M1I4M1I6M2I5M1I5M1D8M4I8M1D7M2D3M3I15M6I1M1I9M1I4M1I6M1I36M1I7M1I18M1D5M1I3M2D20M1I13M4D7M5D2M2D43M1D5M1I12M1D7M1I31M1D13M1I13M1D6M1I1M1I4M3I7M1I31M2I26M1D7M1D8M1I7M1D17M1I18M1D6M1I4M7I13M1D6M1I7M1D31M1I5M1D15M1I20M1D20M1D26M3D2M3D1M9D5M1D24M2I25M1I14M1I5M3I2M1D7M1D3M1D19M1D17M1D16M2D5M5I8M1D15M1D3M2D5M5D15M1I13M3I7M1I9M5D10M2I5M1D10M2D1M1D2M1D9M8D2M1I5M1D6M6I7M1D13M3D7M1D3M1I15M2I18M1I3M1I2M1I5M1I5M2D9M1D1M1D27M1D11M1I16M8D1M2D8M1D15M1D6M1D10M1I24M1I3M1I19M1D12M1D24M1I8M1I2M1I2M1D6M1I31M2D5M5I16M5D5M1D6M3I11M14I12M3D29M1D12M1D5M23D2M1D4M4D6M1I41M2D21M1I17M1I5M1I25M3D18M1I6M1I5M1I42M1D3M1I31M1D3M1I14M1I21M1D8M3I4M1D19M6I10M2D12M7D32M8D2M1I18M2I31M1I15M1D21M1D6M1D3M1D39M2D1M1I10M1I3M1D36M12I45M1I7M1D4M1D1M3D7M1D3M1I5M1I6M1I14M1I14M1D18M1I1M1I6M1D1M2I1M1I4M2I8M1I27M5D20M12I11M1I9M1I29M3I26M2I4M2I3M1D6M37I1M1I4M5I3M1I3M6I3M4I16M1I27M2I3M1I2M2I60M4I5M4D8M21I26M1I16M1I3M1D8M1I22M1D8M10I3M2I3M3I13M36I4M1I40M1D6M1D5M1D7M2D7M1D13M2D2M1I8M2D6M1D9M1D3M1I4M4D3M1I5M1D11M1I4M4I23M1D21M1D17M1I37M2D10M1I36M1I8M1I1M1I9M1D6M1I1M5I1M7I3M2I2M10I2M2I12M1D27M2D1M1I16M1I18M1I25M1I29M1D12M2D18M1D2M3D3M7D13M1I30M3I2M2I18M1I4M2I36M1D19M1I19M1D6M1D4M3I20M2I13M1D61M1D12M3I1M1I6M2I4M2I3M1D7M1I34M1D9M1I5M5I9M3I11M1I4M1D4M1D3M4I2M3I1M8I22M1D10M1I12M1I57M1I25M1I58M4D26M1D2M1D2M1D7M2D43M1D3M1I6M1I9M2I20M1I5M41I5M1I30M1I32M1I12M2D9M4D17M2I44M1I2M1D29M14D1M1D17M1D8M1I27M4D14M1I9M1I4M1D6M1I12M5I26M3D2M1D2M1D18M