@jbrowse/plugin-alignments 1.6.6 → 1.6.9

package/dist/util.d.ts

@@ -1,4 +1,6 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AugmentedRegion } from '@jbrowse/core/util';
 export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
@@ -13,3 +15,5 @@ export declare const orientationTypes: {
     };
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
+export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
+export declare function shouldFetchReferenceSequence(type?: string): boolean;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.6.6",
+  "version": "1.6.9",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,7 +35,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bam": "^1.1.14",
+    "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.1",
     "@material-ui/icons": "^4.9.1",
     "abortable-promise-cache": "^1.5.0",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "9fcca7793af0df2d6e527ddaace2b368c8ed2879"
+  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
 }

package/src/BamAdapter/BamAdapter.ts

@@ -38,7 +38,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
       const bamLocation = readConfObject(this.config, 'bamLocation')
       const location = readConfObject(this.config, ['index', 'location'])
       const indexType = readConfObject(this.config, ['index', 'indexType'])
-      const chunkSizeLimit = readConfObject(this.config, 'chunkSizeLimit')
       const bam = new BamFile({
         bamFilehandle: openLocation(bamLocation, this.pluginManager),
         csiFilehandle:
@@ -49,8 +48,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           indexType !== 'CSI'
             ? openLocation(location, this.pluginManager)
             : undefined,
-        chunkSizeLimit,
-        fetchSizeLimit: 100_000_000,
+
+        // chunkSizeLimit and fetchSizeLimit are more troublesome than
+        // helpful, and have given overly large values on the ultra long
+        // nanopore reads even with 500MB limits, so disabled with infinity
+        chunkSizeLimit: Infinity,
+        fetchSizeLimit: Infinity,
+        yieldThreadTime: Infinity,
       })
 
       const adapterConfig = readConfObject(this.config, 'sequenceAdapter')
@@ -139,7 +143,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
 
     const seqChunks = await features.pipe(toArray()).toPromise()
 
-    const trimmed: string[] = []
+    let sequence = ''
     seqChunks
       .sort((a, b) => a.get('start') - b.get('start'))
       .forEach(chunk => {
@@ -149,10 +153,9 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)
         const trimLength = trimEnd - trimStart
         const chunkSeq = chunk.get('seq') || chunk.get('residues')
-        trimmed.push(chunkSeq.substr(trimStart, trimLength))
+        sequence += chunkSeq.substr(trimStart, trimLength)
       })
 
-    const sequence = trimmed.join('')
     if (sequence.length !== end - start) {
       throw new Error(
         `sequence fetch failed: fetching ${refName}:${(
@@ -181,7 +184,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
 
       for (const record of records) {
         let ref: string | undefined
-        if (!record.get('md')) {
+        if (!record.get('MD')) {
           ref = await this.seqFetch(
             originalRefName || refName,
             record.get('start'),

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -4,18 +4,13 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { BamRecord } from '@gmod/bam'
-import {
-  parseCigar,
-  generateMD,
-  cigarToMismatches,
-  mdToMismatches,
-  Mismatch,
-} from './MismatchParser'
+import { getMismatches } from './MismatchParser'
 
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {
-  private cachedMD = ''
+  // uses parameter properties to automatically create fields on the class
+  // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
   constructor(
     private record: BamRecord,
     private adapter: BamAdapter,
@@ -70,18 +65,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     return this.record.getReadBases()
   }
 
-  _get_MD() {
-    const md = this.record.get('MD') || this.cachedMD
-    if (!md) {
-      const seq = this.get('seq')
-      if (seq && this.ref) {
-        this.cachedMD = generateMD(this.ref, this.get('seq'), this.get('CIGAR'))
-        return this.cachedMD
-      }
-    }
-    return md
-  }
-
   qualRaw() {
     return this.record.qualRaw()
   }
@@ -100,8 +83,6 @@ export default class BamSlightlyLazyFeature implements Feature {
             prop =>
               prop.startsWith('_get_') &&
               prop !== '_get_mismatches' &&
-              prop !== '_get_skips_and_dels' &&
-              prop !== '_get_cram_read_features' &&
               prop !== '_get_tags' &&
               prop !== '_get_next_seq_id' &&
               prop !== '_get_seq_id',
@@ -154,63 +135,14 @@ export default class BamSlightlyLazyFeature implements Feature {
     }
   }
 
-  _get_skips_and_dels(
-    opts: {
-      cigarAttributeName: string
-    } = {
-      cigarAttributeName: 'CIGAR',
-    },
-  ) {
-    const { cigarAttributeName } = opts
-    let mismatches: Mismatch[] = []
-    let cigarOps: string[] = []
-
-    // parse the CIGAR tag if it has one
-    const cigarString = this.get(cigarAttributeName)
-    if (cigarString) {
-      cigarOps = parseCigar(cigarString)
-      mismatches = mismatches.concat(
-        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),
-      )
-    }
-    return mismatches
-  }
-
-  _get_mismatches({
-    cigarAttributeName = 'CIGAR',
-    mdAttributeName = 'MD',
-  }: {
-    cigarAttributeName?: string
-    mdAttributeName?: string
-  } = {}) {
-    let mismatches: Mismatch[] = []
-    let cigarOps: string[] = []
-
-    // parse the CIGAR tag if it has one
-    const cigarString = this.get(cigarAttributeName)
-    const seq = this.get('seq')
-    const qual = this.qualRaw()
-    if (cigarString) {
-      cigarOps = parseCigar(cigarString)
-      mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))
-    }
-
-    // now let's look for CRAM or MD mismatches
-    const mdString = this.get(mdAttributeName)
-    if (mdString) {
-      mismatches = mismatches.concat(
-        mdToMismatches(mdString, cigarOps, mismatches, seq, qual),
-      )
-    }
-
-    // uniqify the mismatches
-    const seen: { [index: string]: boolean } = {}
-    return mismatches.filter(m => {
-      const key = `${m.type},${m.start},${m.length}`
-      const s = seen[key]
-      seen[key] = true
-      return !s
-    })
+  _get_mismatches() {
+    return getMismatches(
+      this.get('CIGAR'),
+      this.get('MD'),
+      this.get('seq'),
+      this.ref,
+      this.qualRaw(),
+    )
   }
 
   _get_clipPos() {

package/src/BamAdapter/MismatchParser.test.ts

@@ -1,9 +1,8 @@
 import {
-  generateMD,
   getMismatches,
   cigarToMismatches,
-  parseCigar,
   mdToMismatches,
+  parseCigar,
   getNextRefPos,
   getModificationPositions,
 } from './MismatchParser'
@@ -29,48 +28,58 @@ test('md to mismatches', () => {
   ])
 })
 
-test('get mismatches', () => {
-  // simple deletion
-  expect(getMismatches('56M1D45M', '56^A45', seq)).toEqual([
-    { start: 56, type: 'deletion', base: '*', length: 1 },
-  ])
+describe('get mismatches', () => {
+  it('simple deletion', () => {
+    // simple deletion
+    expect(getMismatches('56M1D45M', '56^A45', seq)).toEqual([
+      { start: 56, type: 'deletion', base: '*', length: 1 },
+    ])
+  })
 
-  // simple insertion
-  expect(
-    getMismatches(
-      '89M1I11M',
-      '100',
-      'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTA',
-    ),
-  ).toEqual([{ start: 89, type: 'insertion', base: '1', length: 0 }])
+  it('simple insertion', () => {
+    // simple insertion
+    expect(
+      getMismatches(
+        '89M1I11M',
+        '100',
+        'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTA',
+      ),
+    ).toEqual([{ start: 89, type: 'insertion', base: '1', length: 0 }])
+  })
 
-  // contains a deletion and a SNP
-  // read GGGGG--ATTTTTT
-  //      |||||   ||||||
-  //      GGGGGACCTTTTTT
-  expect(getMismatches('5M2D6M', '5^AC0C5', 'GGGGGATTTTTT')).toEqual([
-    { start: 5, type: 'deletion', base: '*', length: 2 },
-    { start: 7, type: 'mismatch', base: 'A', altbase: 'C', length: 1 },
-  ])
+  it('deletion and a SNP', () => {
+    // contains a deletion and a SNP
+    // read GGGGG--ATTTTTT
+    //      |||||   ||||||
+    //      GGGGGACCTTTTTT
+    expect(getMismatches('5M2D6M', '5^AC0C5', 'GGGGGATTTTTT')).toEqual([
+      { start: 5, type: 'deletion', base: '*', length: 2 },
+      { start: 7, type: 'mismatch', base: 'A', altbase: 'C', length: 1 },
+    ])
+  })
 
-  // 0-length MD entries, which indicates two SNPs right next to each other
-  // "They generally occur between SNPs, or between a deletion then a SNP."
-  // http://seqanswers.com/forums/showthread.php?t=8978
-  //
-  // read GGGGGCATTTTT
-  //      |||||  |||||
-  // ref  GGGGGACTTTTT
-  expect(getMismatches('12M', '5A0C5', 'GGGGGCATTTTT')).toEqual([
-    { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
-    { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
-  ])
+  it('0-length MD entries', () => {
+    // 0-length MD entries, which indicates two SNPs right next to each other
+    // "They generally occur between SNPs, or between a deletion then a SNP."
+    // http://seqanswers.com/forums/showthread.php?t=8978
+    //
+    // read GGGGGCATTTTT
+    //      |||||  |||||
+    // ref  GGGGGACTTTTT
+    expect(getMismatches('12M', '5A0C5', 'GGGGGCATTTTT')).toEqual([
+      { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
+      { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
+    ])
+  })
 
-  // same as above but with the non-0-length MD string
-  // not sure if it is entirely legal, but may appear in the wild
-  expect(getMismatches('12M', '5AC5', 'GGGGGCATTTTT')).toEqual([
-    { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
-    { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
-  ])
+  it('non-0-length-MD string', () => {
+    // same as above but with the non-0-length MD string
+    // not sure if it is entirely legal, but may appear in the wild
+    expect(getMismatches('12M', '5AC5', 'GGGGGCATTTTT')).toEqual([
+      { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
+      { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
+    ])
+  })
 })
 
 test('basic skip', () => {
@@ -224,268 +233,15 @@ test('clipping', () => {
   ])
 })
 
-test('md generation', () => {
-  const query =
-    `CACACTAGCCCGTCAGCGAACGCGTGCGCGGCCGCTGCCCTGCAGCGAATGGGGCTAACGACGCATAAAACGCCCGCATA
-ACCACTCGAGCTACGGGAAATTCACTCAGGCTGTGTTGCTTCGACGTGTAGATCTCATTCACATATCATAATACCTCCAA
-GACCAACGGCTGCTCATGACTCTCTTACCTTGTTAGGGACATTTCGGCACTAGGGAAGAGCTGAGGACTTTGAAAACGTC
-GATAAAACCATCGCGGGAACTAGCCTGCGTTAGAACTCCCATATTTTACGGGTCGCAAGCTTGAGAGTCCTGTCCCGGCA
-GCTGCAAGTGCTACGGCAGGAGGGGATCTACCATAACGTGCAGTAAGACCCCTGCCCGTAATGAGGCGGTACTCGTCTCT
-AATCGTCAGTAGTTACTATGTCCGAGGACGTGCCTCTACGAGTTGAACTCTGGCTAGGCCCACCTGTCCGCGCCACTGCT
-CGGGTACCCCATCTGCTTTATCCAACTTCACCTGCGCCTTAACGGAATCTCTGGTTGCCAGTCATCCGATGGTCATTAAG
-CAGCGTGGTACATCGTAAGCCAATACTTCAGGGCGCCTAGCCATATTCCCAGCCAAGCGGCTGCATAATTACAAGCGCTG
-GCACGACTAATCGATCCCACGAAGCCTGGGAGATGACCCTAGCCCTAAAAGTCTGCCCTCGTGACCTATCTGCCACGTGA
-TACTTGATATATTTGTAATGAGCGGAGCAGGGTAGATGACTAATATACAGGGTCGTCTAGGTTTGCACGAATGCAGACAT
-CATCCGCGCAAGGCCCGGACGGCTGTACTCACACAAGCGTAGGTCTCCATTCTCCCTCAGCCAGCACTAAGATTCCCACG
-TGACCAGGGCGACGGGCCCTCAGCCAAACGTATACCTTGATATCTACTTAAGTCAAGGTTGACTCCGAACCCTATGGGTC
-GGTGCCGTTAACAGGGAGTCTATAGTCTCGGCGTTTCCATTGTTGTTTCAAACTCCTGCTTATAAGGGTGAAAGCGCTGG
-AGGGCATAGTTTATGCCCAAAGTTGCGCGTAGATCCGTCGGGATAGTGTGCTATAATAAGGACTGCTCGAGGTGTAGGCG
-GTAACGGCTCCCGCCTTCAGTAGGGCGCGGAACTCGAATCGGAGTTACAGGACTTGACCCGAGTCATATCCAAGTTTATG
-TTAGCCCGATCGGATCTCGGATGCTCGTATCTGCGACGAGGTCGAAGACGGACGAAATACGATTCAACCGCGCGAACCAT
-TGCATCTAACCTTTAGCCTCAATGGGTGTTAACGTGGTGGTGCTCACTGGTCGTACTCTTTTGTGCAACTACTTCCAGTA
-TGAACAACAGTCAAGTTGCGACATGATGCCTCTTTACGTGATTCCCACAGTTTCCCACCTCAGGATGCTTGCTTCTTTAG
-CTAAACCCAATAGTTATGGCGGCCACCTTCAGACGTCCCACGAGGACGGCTATGACGTTGCTAAACGCATTCGCCGCCGA
-AAGGTAGCGCTAACGAGTTCTGTAGAGTTTGTTCCGGGCCAGATCTCCAGGATGGTCGCAACAACGCAGTACCGGTTTTA
-TACTGGTGAACCCTCTACCTGTTATTAAGTTTACAGCGTTGTCCTACGGTACATGGTCGTGAGTACTCGCGTAGTCAAAC
-GCCAGGACTAGCAGCGAGAATTATTGGTCGCGATACTTACTACAATAACTTACCCGATATTGACAGTGCAGGGTTGAAAG
-AGATGGACAGTTGAATATCTACTTTTGACGGAATCCTCAAAACTCCCTCCACCTACAGGTAACGGCCCTGTCCGGGACCG
-CTTTCTTGCATATATTGGTTTCCACAGAGCGTATCTAAGTTAGTCTCTTGACCGTTCACCGACTCTAGGGCGACTCGTTA
-TCGCCCTCCGAAACGATGCTATTCGTTACCTCAATGATGACAGTTGGTCAGACGTAAGTGATCCCAATCTCACTCGTGCC
-TTGTCCACCAGTTCCGTGAAGACGAAGCAATACGCGGAATACGTGGCTTCGTAATATTTTGACGATATGGGGCTGGGACG
-CTCAAGACTTCCAGTGACAAACAAAGTGAAGAGCAACTTGCATCCCTCATCATGACACTATTACCAGAGTAGCCGATGGA
-TTAACGCTAATTTGGTCAGGGCAGCTATCGCATCCCGCAGGTGTAGGCGGAGACTTTTTTTTTTTGCGAGTTGACAGGTA
-ATCTCACGGTATAAGCACGGTTATTTACGCAAGCGACGTCCCTGGGAGAATCCGCCCACGGTAGGACCCCATAATCCATA
-AATACTGCGGTCGAAACCGTTCATATCGTGATCAGGAACCTGCTTTCTAGGGATGCGGTCCCCGCATTCAGAGTTCTACT
-TTGGCCAGCGTGAGACGTTAACAACCCACTTACGCGGTACATTGAAGTCGTTCGAGTCCAGTGTGACCTGTGTACCGAAT
-AACGTGTAGACCAGCGCGTCTACGACTTAGCGCGGCTCCACTCCAAAGCACCTTTTGGGACTTTGCCAACGAGCCTGTTG
-GCCGTTAAGCGGTATTTGCACAAACTAGATCACCCTAGTGTCGGTAACCGACTCACCCTATTGGGATCATCGTGAGCTCG
-AAACACTAGGCGGACCAACGGATGAGCATTTGATTCGGCTCTACAGAGCTTGTCGCCAGAGAAAAACTGTGGCAACTCTA
-CGCTCGCGGGGAATTGACTTTAGCGGCCCCCTAGACAGGTGTGGGACACCTAGTCTAGATTCACGTCCTACACGACATAA
-CAGCACCTTCCTGGCCAGCCCAGAAATATGTACCTGGACGACACTCCAGTCCTTCCGACGCCATAATGTGAGCCGTAGCG
-CCCACGACGATCAACGAGGAGAAATTTACAAAGGCTAGTGTGAATGCTACGTCGTCTACCCATTGCTCCATCGAAACGAA
-CGCAACGCACAGCATACAACGTTCTACCATGCCGGAGCGCGGATCCTCAAGTACAGAAAACAGTAGGTCTAAACATGATC
-CGAACAAATCGGTAGGTTTACACAGCTACCTCCGTCCATATGGCGTACTGCATCGATCGTGCTTACTACGGTCATCGCCG
-GCCCGCGATGCACGTACGAAGGAATACCCTGTCTGCCCCCGCGCGAGCTTACGCTGTCTCGCACATACCGAGCACTGTCG
-CTTCGAAGCTAAACTATGAGCCCAGCCGAGCTCCTTATGGCCGCAACGCTGGTGCGCCAGTCTGATAAATTCCACACGTA
-CACGATCCTCGTGTAAGATCTCGGGCAGTAGTAAGTCATTATCACATGGTTAGGAGATGATAGAATACATGGGTTCTGGT
-AGCTACAACACAGGATTTGTGAACCCTTGGCCCTTTGGTGAGTGCTACAATAAAATTCTCCGTATGGGACTAACCTAAAG
-GGTGCTGCGATTGACTTCCCGGCCCAGGTTAGATGTCCATATCATTCATACATTCCCGACCGACCCAATGCCTAAATCAG
-AGGCGCCTTAGCTAGTTCTTGTATGTGTGCCACGATCCAGGCCACGCAGACACGACCCCTCGGCGAGTGATCACCATTAC
-CGGATTTGGCATCGAAGTCTTTTTCTGGGAAGTTAGCCAGTTTGGTGTGCGGTGCTTAGAATCTTATTCCCAGTCAAACG
-CCCCTGAGGACGAATTGCTATACCCTAGTTGCCACGCCGGAACCATCTTCGGGAGAGTAGACAAATCCGAGTTAGATATG
-TTAGCGTCTTCGTGGAGTCTGAAATGTATCACTTCTACCAGCAGAATACGCGAATGTCTGTTTGCCCTGGATGAGCGGAA
-TTGGCTTAAAAGCACAGACTACGAGCATTTTGAGTACGGTTCCATATCGCGATGTAATTACCTATACTAGGTTATCGCTA
-GTACGAATAGCGAAGTACAGTGTAGCAGGCCCTTTGTTAGCAAGTTGCTCTAAACAGTTGTCAATACGTAGGCACAATAG
-TGCGATATCTTCCTAAATCCGGGAAGCCATGGCGCTGGGCAGAATATCACATACGGAATAATCAACCTCCATATTTGGTT
-CGTTTTACTCGATGAGTGCCCCTTGCTTGAGACGAGCGTTCTGAGTTGATGGCATGTCGAAAGGTTTACGCGGTGAGTAG
-AGCACTCTTGACCCCTACAGATCGGAATCCTCGGAGGTAGGACAGTTGGAACTTCACAGTTAACCTTTGTTCGATTGCAT
-GAAGGTTGTGTTCTGGGAGTAGGCTCCCAAGGTAGCGGTTCATGCCTGGGGGCAGCCCTAAGTTTGTATATATGTGAGTT
-TGCGTCTGAACACATTATAGCATGAGGAAACGTAAGCTTTCTGGAGGGATCTTCTAAAGCCAGGTATCGCCCGCTACGAT
-GCCGGAGCGCAGGGTGGATTCACAGCTACCTCGTGCCTCAAAGGCTTAAGGCTAATCCATAGCAACAGTGCGAAAGGACG
-TCCTTTCAGATTTCGAAAGGTGCTGACACATACAAGGGTCAGGGCGGTCCTACCCTTCTGATGTCCCTACCTGGTTTTTT
-AGCAAGGGTCAAGGCTAGGCTTATACTCCCGAACGCTTTAAACATCTATTCCCACCCCTGACGGGGGGAAGTTGCCGCGT
-TAAGTATAAGAATAAGATTTAACAGTACACTTTAGGTTCCTCTTCCGCGAGCCGTCATACAGCACCGAGCGCCGTTGAAA
-CGCAATTAACGCGTATTTGTCGCTGCGAAAAAAAAACGCTCGCCAGCATATTGGAGTGTCGACTTGAAATATTGAACAAC
-ACCGCATATCAAGACGAATAGTAGGGCTTCACTACCTCCACCTGACGGCCCTAGGACTTATACTCGAAAAAGACCTTCCA
-TCACGATGTCCCTTACCGGCGAGAGTGCTATAATACGCATGAATAGCAGATCTTGCCGTCGCTGAGTGTCACCCAGGGTT
-GCTCCCAGAAAGAGATAGGGCGGAGAGCCATCGACAGCAGCTCTCGATCTAGGTGGTAGCAGGCTAAGGAGTCGTGTCGT
-CGCGCCCGAGTTGGAACCATTATCGATGTACATCAATGCAGTGAATGATGCTGATAGACTCGGGAGTTTGCCTCAAAACC
-CCAGAGTTACGTAGAAGACGCAGGTCTATTAGTTAGAAGGAGTCAGTATTGGCCTTTGAAAGATCTTATGCTCATGCCCT
-AATCGTAGTTAAACGGCGAATCCGTGGAAGGCCAATCTGGCCGGTTTTGACCCCCGGACTCTTAAGACGTCCAATGTGGC
-TAGACATAAGTCAACGAATTACCTATACCGAGGGCGGGAACCGGCCAATTTATTACGAGAGCACGAGAGCCTTGTAGCGA
-CCCAGCACACTAGTCCTCGAGTCCCTCTCATCCTGAGACGTAGAATAGCATATACCGCCTAGGAGAGAATGAGCGCGTCT
-AGGCTTCCGTCGCCCTCTCCGTCGTCTCGGGTGAACCGTAAGTCCTTCCGCATTCCCTTACCTCAAGCGCGTTGGTGTGA
-AGTGGTATTGAGGCCCAGTCTCTATAACGCATATACTTGTGCACTCTATTACTTACCATGGGAACCAATGGCACTCTACG
-AATCATGCTCACAGCTGAGCAACGGTGCTGCTCACCAATTACATATGAGCTCGTGGATTTAGCGTTGGAGCGGAACGATG
-AATTTCCATCTGTTCGCGCGCATCCACTAATCCAATATACGGTTATCCCGAGCGCTACTAGTGTCTGACCGGGTTGGTAG
-CCGAACCCTTTTGCAAGCCGCGCTTAGTGGATGTTGAAGTGGGAGTGATAAGCTTAAGCCGCCACGTTCGGGGGGGACTC
-GTTTATATTGGTGCTGGAATTACGAACGGCGTGATTCGTAGTCGGCCCTAATCGGGCGCGACCGAACACATGTAGTACTG
-TCGAGGCGGTTTAAACCCCCACAGTAGGTACTCTATCAGCAGAATTATGCTAGAAAGTTTCACACACAACTTTCCGCATG
-AGGCTCATGCGGAGCGTCGCACTCCCAATGGCCAGTGCCGGTAGTCGATGTTTGGTCGGAACTTAGTTCCTTCGGAATAA
-CGAACCGGATTTAAAAGAGCCTCAGGAGAACCTAAACGAATCCGTACGCATCTTGCCCAAGGTTGCTGAGCCTCGTCGCC
-TTTCTCAGTTCCACCTACATTAATGCAATGCGTTCGAAGCTTGACCTGCAAACAGGAATCAAGTTCAGACAGAGTGCAAG
-AGTTTCGCAGATAATTGGGAGACGACCCACTTGGATATAGGTGCTTTTTGAGATGTGTGTACGACCGTCCTTTCGAGCAT
-ACCTACGGGTTACAATTGCTCCGGTAAGTCAGGCACATAGAAAACATAGCCACTACTGAGGTGTATCAAGATTACCTCAT
-GTAGACTTGAAATACAGCACATCCGCTTTAAGCTTAACCGATGTAGAACAGCATTTTGGGCGGCGTTGACAGCGTGGCCC
-GCTCACCGGTTTGCTCCCTTCTCACCAAATAACCAATGAGCACGACTTTGGTGACTGGACTGCCAGATGACGGCTACAAC
-CCGTTTTTGGTTCCGAATTCCGCTCTAACTCAACTAACATCCATACTATATGCGCCAGGATATTCTCGCGGTTGGACCCC
-CCTGCCAATTCGGGTTAAAACCACTCCGCACCCCCATGTAGGGGAGCTGGGCCCGCATTACAATATGCGAATCGATCCCG
-CAGATGGACGCTCACAAAATTCAGTCCTTTCACGACTCCGCTCATATAGACGGTAGAAGGGATACTGAGGCTGTTAGATA
-GGACGTCGAGCATGGCGTAGACGAGCGCAACCGGGTCGAAGGCCCGCATTACCGTGACACCCAGTTGAAAGGATTTACAC
-TGCTTCATATCGATATTTACCACTTTGTAATTGGGAGCTCAAAGACCTAAGTCAACACGGACCATCATACAGGGTCGCCA
-GTAAATGAGAAGCGCTGTCTGTGCCATGGAGAAGCGCTGCTACAGCACACAACGAACAATCTGCATGTGAAGGAGGGTGC
-CTCTTTTGGGATGAGCCTACGGGGATGTGTATCCCATGCCCTGTAGGCAGTTGGGACTAGCGCCGAGCTAATCTAGTAAC
-TAAGGCGCCAGCCGCGGCTGTTTGCCGAAGTCGTGCTGACTGCTGTACAACGAAGGGCGAGCGTGTTAACATGCCTACAC
-GTTGACCTAGACTAGTCCAAGTTCTGAAAGTCCCATTAGGTCCGGGTAGTACAGTCCTCGGTTCCAGTCCCATCTTGTGC
-CGCCAAGGACAAGCGATCATCAAAATCTGACTGAGTAATTGAATCAGCTACCTCAGACCACATTCAGCTCTCGGTAAACA
-TGCGATGGCTTGTGGTTGCACCGTAAAAGGGGGAAGCCCATCCATCCTGTAACACCACAATCGCGCGTAGCTTAATAACG
-GCTCCACCATTAGAATTCGATCGAGAGACACTGGTTTCAAGAGCCTTCCCTTTTGCTTTAGTGGGCCAAATCGCAACCCT
-GCTCCCCTCCCTTACGCCTTATACACTTCAGTGCAAATTCATCGCGTTCGAGCGAACAACCTGGACTTCTGTTGTACGTA
-GTCCACGGGGGCTTTATTCATTATAGAAAGCCCCCTACTGTACACCGTTTATCATGGTTCACATCATGAGCTGATCACCT
-AGAGAGTCGTCATGCACATTCGCACTAACAAGGACATATGAGTAACCGGGAGAG`.replace(/[\r\n]+/gm, '')
-
-  const target = `cacactagccccgtcagcgacggtgcgcggccgctgccctgcagcgaatggggctaacac
-gcataaaacgcccgcataaccactcgagctacgggaattcactcaggctgttgcttcgac
-gtgtagtctcattacataatcataatacctccaagaccaacggctgctcatgactctctt
-accttgttagggacatttcggcactagggaagagctgaggactttgaaaacgtcgataaa
-accatcgcgggaactagctgcgttagaactccatattttacgggtcgcaagcttgaggtc
-ctgtcccggcagctgcaagtgctacggcaggaggggatctacctaacgtgcagtaacgag
-cccctgcccgtaatgaggcgtactcgtctctaatcgtcagtaagttactatgtccgagga
-cgcctctacgagttgaactctggctaggcccacctgtccgcgccctgctcgggtacccca
-tctgcttatccaacttcacctcgccttacggaatctctggttgccagtcatccgatggtc
-attaagcagcgtggtacatcgtagccaatacttcagggcgccagccatattcccagccaa
-gcggctgcataattacagcgcctggcacgactaatcgatcccacaagcctggtagatgac
-ccttagccctaaagcgccctctgacctatctgcacgtgatacttgattatttgtaatgag
-cggacagggtagatgactaatatacagggtcgtctaggtttgcacaatgcagacatcatc
-cgcgcaaggcccggacggctgtactcacacagctagctccatctccctcagcagcactaa
-gattcccacgtgaccagggcgacgggcctcagccaaacgtatccttgatatctacttaag
-tcaaggttgactccgaaccctatgggtcggtgccgttaacagggagtctatatctcggcg
-ttccattgcttgtttcaaactcctgctataaggtgaaagcgctggagggcatagtttatg
-cccaaagttgcgcgtagatccgtcgggatatgtgctataataaggactgctcgaggtagg
-cggtaacggctcccgccttcagtaggcgcggaactcgaatcggagttacaggacttgacc
-gagtcatatccaagtttatgttacccgatcggatccggatgctcgtatctgcgacgaggt
-cggaagacggacgaaatacgattcaaccgcgcgaaccattagcatctaacctttagcctc
-aatgggtgttaacgtggtgggctcactcggcgtactctttgtgcaactattccgtatgaa
-caacagtcaagttgcgacatgatgctcttacgtgattcccacagtttcccacctcaggat
-gctttctttagctaaacccaatagttatggcggcaccttcagactcccacgaggacggct
-atgacgttgctaaaccattcgccgccaaaggctagcgctaacgagttctgtgagtttgtt
-ccgggccagatctccaggatggtcgcaacaacgcagtaccggttttatactggtgaccct
-ctacctgttattaagttacagcgttgtcctacgtacatggtcgtgagtactcgcgtagtc
-aaacgccaggactagcagcgagaattattgtcgcgatacttactacaatacttacccgat
-attgacgtgcagggttgaaagagatggacagttgaatatctattttgacggaatcctcaa
-aactccctccacctcaggtaacggccctgtccgggaccgcattcttgcatatattggttc
-ccagagcgtatctaagttagtctcttgaccgttcaccgactctagggcgactcgttatcg
-ccctccgaaacgatgctttcgttacctcaatgatgacaggctgtaacgtaagtgatccca
-atctcactcgtgccttgtccaccgttccgtgaagacgaagcaatacgcggaatacgtggc
-ttcgtaatattttgacgatatggggctgggacgctcaagacttccatgacaaacaaagtg
-aagagcaactgcatccctcatcatgatcactattaccagagtagcgatggataacgctaa
-tttggtcagggcagctatcgcatcccgcaggtgtaggcggagactttttcttttgttgcg
-agttgacaggtaatctcacggtataagcacggttatttacgcaagcgacgtccctgggag
-aatccgcccacgtaggaccccataatccataaatactgcggtcgaaaccttcatatcgtg
-acagaaccgctttctagggatgcggtccccgcattcagagttctactttggccagcgtga
-gacttaacaactccacttacgcggtacattgaagtcgttcagtccagtgtgacctgtgta
-ccgaataacgtgtagaccagcgcgtctacgacttagcgcggctccactccaaagcacctt
-ttgggactttccaacgagcctgttggccgttaagcggtatttcacaaatagatcacccta
-gtgtcggtaaccgactaccctattgggatcatcgtgagctcgaaacactagaggcggacc
-aacggatgacatttgattcggctctacagagcttgtcgccagagaaaaactgtggcaatc
-tacgctcgcggggaattgactttagcggcccctagacaggtgtgggacactagtctagat
-tcacgtcctacacgacataacagcaccttcctggccagcccagaaatagtacctggacga
-catccagccttccgacgccataatgtgagccgtagcgcccacgacgatcaacgaggagaa
-atttacaaaggctgtgtgaatgctacgtcgtctaccattgctcatcgaaacgaacgcaac
-gcacagcatacaacgtttaccatgccggagcgggatcctcaagtacagaaaacagaggtc
-taaacatgatccgaacaaatcggtaggtttacacagctacctcgtccattggcgtactgc
-atcgatcgtgcttactacggtcatgccggcccgcgatgcacgtacgaaggaataccctgt
-ctgcccccgcgcgagttacgctgtctcgcacataccgagcactgtcgttcgaagctaaac
-tatgagcccagccgagctccttatggccgcaacgctggtgcggccagctgataaattcca
-cagtacacgatcctcgtgtaagatctcgggcatagtaagtcatttcacatggttaggaga
-gatagaatacatggttctggtagctcaaccaggatttgtggaacccttggcccttggtga
-gtgctacaataaaattctccgtatgggacaaccaaagggtgctggatgtgacttcccggc
-ccaggttagatgtccatatcattcatacattgcccgaccgacccaatgcctaaatcagag
-gcgccttagctagttcttgtagtgtgccacgtccggccacgcagacacgaccctcggcga
-gtgatcaccattaccggattggcatcgaagtctttttctgggaagttagccagtttggtg
-tgcggtgcttagaatcttattcccagtcaaacgcccctgggacgaattgctaaccctagt
-tgccacgccggaaccatcttcgggagagtagacaaatccgagttagatatgttagcgtct
-tcgtgagtctgaaatgtatcacttcaccgcagaatacgcgaatgtctgtttgccctggac
-tgacggaattggcttaaaagccgactagagcattttggtacggttcctatccgcgatgta
-attacctatctaggttatcgctagacgaatagcgagtacagtgtagcaggccctttgtta
-gcaagttgctctaaacagttgtcaaaacgtaggcacaatagtgcgattcttctaaatccg
-ggaagctcatggcgctgggcagaaatatcacatacgggaataatcaacctccattttggt
-tcgttttactcgatgagtgccccttgcttgagacgagcgttctgagttgatggcatgtcg
-aaaggtttacgcggtgagtagagcactttacccctacagatcggaatcctcgaggaggac
-agttggaacttcacattaacctttgttcgattgcatgaaggttgtgttctgggagtaggc
-tcccaaggtagcggttcatgctgggggcagccctaagtttgtattatgtgagtttgcgtc
-tgaaactacatttagcatgaggaacgtaagctttctggagggatcttctaaagccaggta
-tcgcccgctacgatgccggagccggtggttcacagctacctgtgctcaaaggcttaaggc
-taatcatagcaacagtgcgaaaggacgtctttcagatttcgaaaggtgctgacacaacaa
-gggtcagggcggtcctacccttctgattccctacctggttttttagcaagggtcaaggct
-aggcttatactcccgaacgctttaaacactatcccacccctgacggggggaagttgcgcg
-ttaagtataagaataagatttaacagtacactttaggttcctcttccgcgagccgtcata
-cagcaccgagcgccgttgaaacgcgattaacgcgtattgtcgtgcgaaaaaaaaacgctc
-gccagcatattggagtgtcgacttgaaatattgaacaacaccgcatatcaaggacgaata
-gtagggcttcactacctccacctgacggccctaggacttatactcgaaaaagaccttcca
-tcacgatgtcccttaccggcgagagggctatatacgcatgaatagcagatcttgccgtcg
-ctgagtgtcacccagggttgctccagaaaggagatagggcggagagccatcgacagcagc
-tctcgtctaggtggtagcagctaaggagtcgtgtcgtcgcgccgagttggaacattatcg
-atgtacatcaatgcagtaatgatgctgatagactcgggagtttcctcaaacccagagtta
-cgagaagacgcaggtctatcagttagaaggagtcagtattggcctttgaaagatcttatg
-ctcatgcccaatcgtagttaaacgcgaatcgggaaggccaatctggcggttttgaccccc
-ggactcttaagacgtccaatgtggctagacataagtaacgaattactctataccgagggg
-cgggaaccggccaatttattacgagagcacgagagccttgtagcggccagcacactatcc
-tcgagtccctctatcctgagacgtagatatacatatacgcctagagagaatagccgtcta
-ggcttccgtcgccctctccgtcgttcgcgtgaaccgtaagtcttccgcattcccttcctc
-aagcgcgttggtgtgagagtggtattgaggcccagtcttataacgcatatacttgtgcac
-tctattacttaccatgggaaccaatggcactctcgaatcatgctcacagctgagcaacgg
-tgctgctcaccaattacatatgagtcgtggtttagcgttggagcggaagatgaatttcca
-tctgttcgcgcgcatcactaaccaatatacggttatcccagcgctatctagttctgaccg
-ggttggtagcgaacccttttgcaagccggcttagtggatgtgaagtgggagtgataactt
-aagccgccacgttcgggggggactcgtttatattggtgctggaatacgaacggcgtgatt
-cgtagtcgccctaatcgggcgcgacaacacatgtagtactgtcgaggcggtttaaaccca
-cagtaggtactctatcagcagaattatgctagaagtttcacaacaactttccgcatgagg
-ctcagcggcagcgtcgcactcccaatggccagtgccggtagcgatgtttggtggaattag
-ttccttcggaatacgaaccggatttaaagagcctcggagaacctaaacgaatccgtacgc
-atcttgcccaaggtgctgagccttgtcgcctttctcagttccacctacattaatgcaatg
-cgttcgaagctctgaccgcaaacaggaatcaagttcagacagagtgcaagagtttcgcaa
-taattgggaacgacccacttgatataggtgcttttagagatgtgtgtacgaccgtccttc
-gagcatacctacgggttacaattgctccggtaagtcaaggcacatagaaaacatagccaa
-ctgagagtgtatacaagattacctcatgtagactgaaatacacacatcgctttaagctct
-caaccgatgtagaacagattttgggcggcgttgacagcgtgcccgctcaccggtttgctc
-ccttctcaccaaataaccatgagacgactttggtgactggactgccagatgacgggctac
-aaccgttttggttccgaattcgctctaactcaactaacatcatactatatgcgccaggat
-attctcgcggttggacccccctgccaattcgggttaaaaccactccccccatgtagggag
-ctgccgcaattacaatatcgacgatcccagatggacgctcacaaaatatcagtcctttca
-cgatccgctcatatagacggatgaagggactgaggctgttagatagtgacgtcgagcatg
-gcgtagacgagcgcaaccgggtcgaggcccgcattaccgtgacacccagttgaaaggatt
-tacactgcttcattcgatatttaccactttgtatgaggagctcaacctaagtcaacacgg
-accatcatacaggtcgccagtaatgagaaggctgctgtgccatggagaagcgctgctaca
-gcacacaacgaacatcttgcaatgtgaaggagggtgctcttttgggatgagcctacgggg
-atgtgtatccctgccctgtaggcagttgggacttagcgcgactatctagataactaaggc
-gccagccgcggctgtttgccgaagtcgtgctgatgctgtacaacgaagggcgagcgtgtt
-aacatgctacacgttgacctagactagtccaagtctgaaagtcccaatttaggtcgggta
-gtacagtcctcggttccagtcccatgttgtgccgacaaggacaagcgatcatcaaatcga
-ctgaaattgaatcagctacctcagaccacattcagctctcggtaacatgggaggcttgtg
-gttgcaccgtaaaagggggatagcccatccatcctgtaaacctacaatcgcgcgtagctt
-aatacgctcacattagacattcgatcgagagacctggtttcaagagccttcccttttgct
-ttagtgggccaaatcgcaaccctgctcccctcccttacgccttatacacttcagtgcaaa
-ttcatgcgttcagcgaacaactggacttctgttgtacgtagtccacgggggcttattcat
-tatagaaagccccctactgtcaccgttatatggttcacacatgagctgatcacctagaga
-gtcgtcatgcacattcgcctaacaaggacatatgagtaaccgggaggg`.replace(/[\r\n]+/gm, '')
-  const cigar =
-    `8M1D10M1I3M1I36M1I37M1I13M2I18M1I7M1I4M1D119M1I13M1I27M1I46M1I13M1D2M1D19M1I22M1
-D19M2I43M1I21M1I16M1I6M1I55M1I20M1I34M1I4M1D23M1I18M1D10M3I8M1I11M1I15M1I17M1I41
-M1I45M1I3M1I3M2I5M1I10M1I35M1I16M1I70M1I8M1I8M1D17M1I5M1I59M1I25M2I29M1I34M1I25M
-1I12M1I26M1D38M1D39M1I17M1I12M1I4M1I31M1I3M1I36M3I30M1I11M1I31M1I36M1I64M1I20M1I
-17M1I57M1I20M1I17M1I36M1I32M1I45M2I78M1I22M2I44M1I83M1I23M1I17M1D17M1I7M1I57M2D8
-1M1I38M1I12M1I2M1I5M1I55M1I8M1D28M1I90M1I32M1I6M1I28M1I33M2D18M1I49M1I30M1I21M1I
-59M1I14M1I5M1I66M1I21M1I8M1I35M1I15M1I23M1I47M1I7M1I35M1I51M1I32M1I54M1D5M1I15M1
-I30M1I12M1I16M1I12M1I13M1I4M1I10M1D13M1I36M1I4M1I11M1I3M1D43M1D49M1I10M1I3M1I16M
-1I28M1I81M1I13M1I72M1I21M1I3M1I31M1D3M1I17M2I7M1I10M1I10M1I3M1D18M1I15M1I10M1I73
-M1I4M1I15M1D15M1D12M1D18M1I91M2I26M1I4M1I20M1I65M1I24M1I20M2D6M1I10M1I60M3I6M1I1
-3M1I3M1I20M1I24M1I28M1I31M1I61M1I3M1I25M1I100M1I6M1I69M1D99M1I51M1I7M1D35M1I14M1
-I22M1I11M1I25M1I26M1I7M2I12M1I67M1I14M1I7M2I16M1I50M1I10M1D9M1D48M1I12M1I15M1I15
-M1D3M1I6M1I6M1I8M1I3M1I30M1I17M1I15M1I20M1D21M1I55M1I51M1I6M1I18M1I27M1I6M1I18M1
-I7M1D5M1I17M1I19M1I12M1I17M1I47M1I23M1I18M2I31M2I36M1I10M1I22M1I4M1D32M1I11M1I4M
-1I16M1I13M1I10M1I38M1I58M1D5M1I42M1I10M1I11M1I37M1I39M1D22M2I6M1D6M1D20M1I9M1I5M
-1I9M2D19M1I23M1I38M1I5M1I30M1D10M2I16M1I20M1I65M4I10M1I8M3I4M1D10M1I3M2I6M2I20M1
-D15M1I25M2I18M1D37M1I49M1I20M2I2M1D8M3I27M1I10M1I9M1I4M1I46M1D15M1I35M1I21M1D5M1
-I3M1I2M1I6M1D43M1I33M1I27M1I13M2D6M1I59M1I5M1I6M2I39M1I9M1I28M1D43M2I5M2I8M1D15M
-1I92M1I6M1I9M1I32M1I28M1I5M1I4M1I10M1I39M1I30M`.replace(/[\r\n]+/gm, '')
-
-  expect(generateMD(target, query, cigar)).toBe(
-    '8^C128^A218^C2^G41^A218^C31T9^T10G0C293^C232^G38^A46C1G176A2G1C308A19C99C1G0T0A161^T81^TC4G196^T217^AG590^G117^G67^G43^G327^C21C28^C94A40^T15^A12^G112T155^AC0T75C301G86^G93G63^G169C70G75^T9^G48G41^T59C48^G209^T261^C134T47^C83A60^A28^A6^A43^CT2C112^G10G122^A39^A32A0T24^T108^A98T0C0T3^A71^T16^A116^AT37G8A74G30^T18A0C1T21C4A7^C268G1',
-  )
-})
-
 test('getNextRefPos basic', () => {
-  const cigar = '10S10M1I4M1D15M'
-  const cigarOps = parseCigar(cigar)
-  const iter = getNextRefPos(cigarOps, [5, 10, 15, 20, 25, 30, 35])
+  const cigar = parseCigar('10S10M1I4M1D15M')
+  const iter = getNextRefPos(cigar, [5, 10, 15, 20, 25, 30, 35])
   const [...vals] = iter
   expect(vals).toEqual([-5, 0, 5, 10, 14, 20, 25])
 })
 test('getNextRefPos with many indels', () => {
-  const cigar = '10S4M1D1IM10'
-  const cigarOps = parseCigar(cigar)
-  const iter = getNextRefPos(cigarOps, [5, 10, 15])
+  const cigar = parseCigar('10S4M1D1IM10')
+  const iter = getNextRefPos(cigar, [5, 10, 15])
   const [...vals] = iter
   expect(vals).toEqual([-5, 0, 5])
 })