Merge pull request #991 from GMOD/gvcf_support

Add more gVCF support

docs/tutorial/data_files/gvcf.vcf.gz.conf

@@ -0,0 +1,6 @@
+[ tracks . volvox_gvcf_test]
+storeClass = JBrowse/Store/SeqFeature/VCFTabix
+urlTemplate = ../../raw/volvox/gvcf.vcf.gz
+category = VCF
+type = JBrowse/View/Track/CanvasVariants
+key = VCF - GVCF test data

package.json

@@ -6,8 +6,8 @@
   "repository": "https://github.com/GMOD/jbrowse.git",
   "scripts": {
     "test": "phantomjs tests/js_tests/run-jasmine.js http://localhost:3000/tests/js_tests/index.html",
-    "start": "utils/jb_run.js -p 8082",
-    "watch": "watch 'npm run build' src/JBrowse plugins",
+    "start": "./jb_run.js -p 8082",
+    "watch": "watch 'npm run build' src/JBrowse plugins tests/js_tests",
     "build": "node node_modules/webpack/bin/webpack.js --config webpack.config.js",
     "hint": "jshint src/JBrowse/"
   },

release-notes.txt

@@ -12,6 +12,9 @@
   * Add ability for the CanvasFeatures feature labels to stay visible on the screen.
     (issue #390, pull #971, @cmdcolin, @rbuels)
 
+  * Improve VCF tracks support for GVCF generated by GATK, and fix a number of related
+    VCF details display bugs. (pull #991, @cmdcolin)
+
   * `generate-names.pl` now supports indexing GFF3 files, enabling better use of
     GFF3Tabix tracks. Thanks to @billzt for the initial implementation!
     (issue #780, pull #900, @rbuels)

setup.sh

@@ -144,6 +144,7 @@ echo -n "Formatting Volvox example data ...";
     cat docs/tutorial/data_files/volvox.sort.gff3.gz.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/volvox.bw.gff3.gz.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/volvox.sort.bed.gz.conf >> sample_data/json/volvox/tracks.conf
+    cat docs/tutorial/data_files/gvcf.vcf.gz.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/bookmarks.conf >> sample_data/json/volvox/tracks.conf
     bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
     bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/volvox/trackList.json

src/JBrowse/Store/SeqFeature/VCFTabix/Parser.js

@@ -3,6 +3,7 @@ define([
            'dojo/_base/array',
            'dojo/json',
            'JBrowse/Util/TextIterator',
+           'JBrowse/Util',
            'JBrowse/Digest/Crc32',
            './LazyFeature'
        ],
@@ -11,6 +12,7 @@ define([
            array,
            JSON,
            TextIterator,
+           Util,
            Digest,
            LazyFeature
        ) {
@@ -112,13 +114,14 @@ return declare( null, {
             };
         }
 
-        if( alt && alt[0] != '<' )
+        if( alt ) {
             featureData.alternative_alleles = {
                 meta: {
                     description: 'VCF ALT field, list of alternate non-reference alleles called on at least one of the samples'
                 },
                 values: alt
             };
+        }
 
         // parse the info field and store its contents as attributes in featureData
         this._parseInfoField( featureData, fields );
@@ -230,7 +233,9 @@ return declare( null, {
         "CNV": { description: "Copy number variable region (may be both deletion and duplication)", so_term: 'copy_number_variation' },
         "DUP:TANDEM": { description: "Tandem duplication", so_term: 'copy_number_gain' },
         "DEL:ME": { description: "Deletion of mobile element relative to the reference" },
-        "INS:ME": { description: "Insertion of a mobile element relative to the reference" }
+        "INS:ME": { description: "Insertion of a mobile element relative to the reference" },
+        "NON_REF": { description: "Represents any possible alternative allele at this location", so_term: 'sequence_variant' },
+        "*": { description: "Represents any possible alternative allele at this location", so_term: 'sequence_variant' }
     },
 
     /**
@@ -360,7 +365,6 @@ return declare( null, {
                                                  return this._find_SO_term_from_alt_definitions( alt );
                                              }, this ),
                                   function( t ) { return t; } );
-
         if( types[0] )
             return types.join(',');
 
@@ -376,7 +380,7 @@ return declare( null, {
         if( ! alt )
             return 'no alternative alleles';
 
-        alt = alt.replace(/^<|>$/g,'');
+        alt = alt.replace(/<|>/g,'');
 
         var def = this.getVCFMetaData( 'alt', alt );
         return def && def.description ? alt+' - '+def.description : SO_term+" "+ref+" -> "+ alt;
@@ -391,8 +395,11 @@ return declare( null, {
 
         // look for a definition with an SO type for this
         var def = (this.header.alt||{})[alt] || this._vcfReservedAltTypes[alt];
-        if( def && def.so_term )
+        if( def && def.so_term ) {
             return def.so_term;
+        } else if( def && (this._vcfReservedAltTypes[alt]||{}).so_term ) {
+            return this._vcfReservedAltTypes[alt].so_term;
+        }
 
         // try to look for a definition for a parent term if we can
         alt = alt.split(':');

src/JBrowse/View/Track/_VariantDetailMixin.js

@@ -45,7 +45,12 @@ return declare( [FeatureDetailMixin, NamedFeatureFiltersMixin], {
 
         return container;
     },
-
+    renderDetailValue: function( parent, title, val, f, class_ ) {
+        if(title == "alternative_alleles") {
+            val = Util.escapeHTML(val);
+        }
+        return this.inherited(arguments, [parent,title,val,f,class_]);
+    },
     _isReservedTag: function( t ) {
         return this.inherited(arguments) || {genotypes:1}[t.toLowerCase()];
     },
@@ -113,7 +118,12 @@ return declare( [FeatureDetailMixin, NamedFeatureFiltersMixin], {
                                            descriptions[k] = subValue[k].meta && subValue[k].meta.description || null;
                                        }
                                        return descriptions;
-                                   })()
+                                   })(),
+                    renderCell: {
+                        "GT": function( field, value, node, options ) {
+                            thisB.renderDetailValue( node, '', Util.escapeHTML(value), f, '' );
+                        }
+                    }
                 }
             );
         };
@@ -141,11 +151,9 @@ return declare( [FeatureDetailMixin, NamedFeatureFiltersMixin], {
             var value_parse = value.values[0];
 
             var splitter = (value_parse.match(/[\|\/]/g)||[])[0]; // only accept | and / splitters since . can mean no call
-            if(alt) {
-                alt = alt[0].split(','); // force split on alt alleles
-            }
+            alt = alt[0].split(','); // force split on alt alleles
             var refseq = underlyingRefSeq ? 'ref ('+underlyingRefSeq+')' : 'ref';
-            value = array.map( splitter?value_parse.split(splitter):value_parse, function( gtIndex ) {
+            value = array.map( splitter ? value_parse.split(splitter) : value_parse, function( gtIndex ) {
                                    gtIndex = parseInt( gtIndex ) || gtIndex;
                                    if(gtIndex == '.') { return 'no-call' }
                                    else if(gtIndex == 0) { return refseq; }

tests/js_tests/spec/VCF.spec.js

@@ -35,6 +35,37 @@ describe('VCF store', function() {
          runs(function() {
                   expect(features.length).toEqual( 560 );
          });
+  });
+
+
+
+
+  it('reads gvcf * alleles', function() {
+         var store = new VCFStore({
+             browser: new Browser({unitTestMode: true}),
+             config: {
+                 urlTemplate: '../../docs/tutorial/data_files/gvcf.vcf.gz',
+                 baseUrl: '.'
+             },
+             refSeq: { name: '1', start: 0, end: 5000 }
+         });
+
+         var features = [];
+         waitsFor( function() { return features.done; } );
+         store.getFeatures({ ref: 'ctgA',
+                             start: 0,
+                             end: 5000
+                           },
+                           function(f) { features.push( f ); },
+                           function( ) { features.done = true; },
+                           function(e) { console.error(e.stack||''+e); }
+                          );
+         runs(function() {
+                  expect(features.length).toEqual( 7 );
+                  expect(features[2].get('alternative_alleles').values).toEqual("TC,<*>");
+         });
+
+
 
   });
 
@@ -46,6 +77,7 @@ describe('VCF store', function() {
                  baseUrl: '.'
              },
              refSeq: { name: 'ctgA', start: 0, end: 50000 }
+
          });
 
          var features = [];
@@ -67,6 +99,36 @@ describe('VCF store', function() {
 
   });
 
+  it('reads gatk non_ref alleles', function() {
+         var store = new VCFStore({
+             browser: new Browser({unitTestMode: true}),
+             config: {
+                 urlTemplate: '../data/raw.g.vcf.gz',
+                 baseUrl: '.'
+             },
+             refSeq: { name: 'ctgA', start: 0, end: 5000 }
+         });
+
+
+         var features = [];
+         waitsFor( function() { return features.done; } );
+         store.getFeatures({ ref: 'ctgA',
+                             start: 0,
+                             end: 100
+                           },
+                           function(f) { features.push( f ); },
+                           function( ) { features.done = true; },
+                           function(e) { console.error(e.stack||''+e); }
+                          );
+         runs(function() {
+                  expect(features.length).toEqual( 37 );
+                  expect(features[0].get('alternative_alleles').values).toEqual('<NON_REF>');
+         });
+  });
+
+
+
+
   it('parses END field', function() {
          var store = new VCFStore({
              browser: new Browser({unitTestMode: true}),