debugString function added (#516)

* debugString is now a member of all Alignment implementations

package.json

@@ -50,6 +50,7 @@
   ],
   "dependencies": {
     "backbone": "1.1.2",
+    "jquery": "3.3.1",
     "d3": "^3.5.5",
     "data-canvas": ">=0.1.1",
     "jbinary": "^2.1.3",

src/main/Alignment.js

@@ -30,6 +30,11 @@ function ga4ghStrandToStrand(str: string): Strand {
   return str && str == 'POS_STRAND' ? '+' : (str && str == 'NEG_STRAND' ? '-' : '.'); // either +, - or .
 }
 
+// builds a cigarString string that is useful to users.
+function makeCigarString(cigarOps: Array<CigarOp>) {
+  return cigarOps.map(({op, length}) => length + op).join('');
+}
+
 export type MateProperties = {
   ref: ?string;
   pos: number;
@@ -52,10 +57,11 @@ export type Alignment = {
   getMateProperties(): ?MateProperties;
   getInferredInsertSize(): number;
   getCoverage(referenceSource: Object): CoverageCount;
-
+  debugString(): string; 
 };
 
 module.exports = {
   strToStrand,
-  ga4ghStrandToStrand
-};
+  ga4ghStrandToStrand,
+  makeCigarString
+};

src/main/GA4GHAlignment.js

@@ -6,6 +6,7 @@
 'use strict';
 
 import type {CigarOp, MateProperties, Strand} from './Alignment';
+import {makeCigarString} from './Alignment';
 import type {CoverageCount} from './viz/pileuputils';
 import {getOpInfo} from './viz/pileuputils';
 
@@ -104,6 +105,13 @@ class GA4GHAlignment /* implements Alignment */ {
       return 0;
     }
   }
+  debugString(): string {
+    return `Name: ${this.name}
+    Position: ${this.pos.toString()}
+    CIGAR: ${makeCigarString(this.cigarOps)}
+    Sequence: ${this.alignment.alignedSequence}
+    Quality:  ${this.alignment.alignedQuality} `;
+  }
 
   getCoverage(referenceSource: Object): CoverageCount {
     return {

src/main/data/SamRead.js

@@ -14,6 +14,7 @@
 
 import type VirtualOffset from './VirtualOffset';
 import type {Strand, CigarOp, MateProperties} from '../Alignment';
+import {makeCigarString} from '../Alignment';
 
 import jDataView from 'jdataview';
 import jBinary from 'jbinary';
@@ -161,7 +162,7 @@ class SamRead /* implements Alignment */ {
   }
 
   getCigarString(): string {
-    return makeCigarString(this.getFull().cigar);
+    return makeCigarString(this.cigarOps);
   }
 
   getQualPhred(): string {
@@ -249,11 +250,6 @@ Tags: ${JSON.stringify(f.auxiliary, null, '  ')}
   }
 }
 
-// Convert a structured Cigar object into the string format we all love.
-function makeCigarString(cigarOps: Array<{op:string; length:number}>) {
-  return cigarOps.map(({op, length}) => length + op).join('');
-}
-
 // Convert an array of Phred scores to a printable string.
 function makeAsciiPhred(qualities: number[]): string {
   if (qualities.length === 0) return '';

src/test/FakeAlignment.js

@@ -40,6 +40,7 @@ class FakeAlignment /* implements Alignment */ {
   getInterval(): ContigInterval<string> { return this.interval; }
   getReferenceLength(): number { return this.interval.length(); }
   getMateProperties(): ?MateProperties { return this.mateProps; }
+  debugString(): string { return this.name; }
 
   getCoverage(referenceSource: Object): CoverageCount {
     return {

src/test/GA4GHAlignment-test.js

@@ -36,6 +36,7 @@ describe('GA4GHAlignment', function() {
       pos: 10007,
       strand: '-'
     });
+    expect(a.debugString().length).to.be.above(0);
     done();
   });
 

src/test/data/SamRead-test.js

@@ -44,6 +44,7 @@ describe('SamRead', function() {
         pos: 79,
         strand: '-'
       });
+      expect(read.debugString().length).to.be.above(0);
 
       // This one has a more interesting Cigar string
       expect(reads[3].cigarOps).to.deep.equal([