More misc

package.json

@@ -43,7 +43,6 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/binary-parser": "^1.3.5",
     "@jkbonfield/htscodecs": "^0.5.1",
     "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",

src/cramFile/sectionParsers.ts

@@ -1,11 +1,8 @@
-import { Parser } from '@gmod/binary-parser'
 import { TupleOf } from '../typescript'
 import { ParsedItem, parseItf8, parseLtf8 } from './util'
 import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes'
 import { CramEncoding } from './encoding'
 
-const singleItf8 = new Parser().itf8()
-
 export function getCramFileDefinition(buffer: Buffer, startOffset = 0) {
   const b = buffer.subarray(startOffset)
   const dataView = new DataView(b.buffer, b.byteOffset, b.length)
@@ -132,11 +129,6 @@ export function getCramTagDictionary(
   }
 }
 
-// const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
-const parseByteAsBool = new Parser().uint8(null, {
-  formatter: /* istanbul ignore next */ val => !!val,
-})
-
 export interface CramPreservationMap {
   MI: boolean
   UI: boolean
@@ -633,7 +625,7 @@ function getCramCompressionHeader(
   }
 }
 
-function cramContainerHeader1(
+function getCramContainerHeader1(
   majorVersion: number,
   buffer: Buffer,
   dataView: DataView,
@@ -642,7 +634,8 @@ function cramContainerHeader1(
   // byte size of the container data (blocks)
   const length = dataView.getInt32(offset)
   offset += 4
-  // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
+  // reference sequence identifier, -1 for unmapped reads, -2 for multiple
+  // reference sequences
   const [refSeqId, newOffset1] = parseItf8(buffer, offset)
   offset += newOffset1
   const [refSeqStart, newOffset2] = parseItf8(buffer, offset)
@@ -668,17 +661,64 @@ function cramContainerHeader1(
 
   let numBases
   if (majorVersion > 1) {
-    const [n, newOffset5] = parseItf8(buffer, offset)
+    const [n, newOffset5] = parseLtf8(buffer, offset)
     numBases = n
     offset += newOffset5
     maxLength += 9
   }
-  parser = parser
-    .itf8('numBlocks') // the number of blocks
-    .itf8('numLandmarks') // the number of landmarks
+  const [numBlocks, newOffset6] = parseItf8(buffer, offset)
+  offset += newOffset6
+  const [numLandmarks, newOffset7] = parseItf8(buffer, offset)
+  offset += newOffset7
   maxLength += 5 + 5
 
-  return { parser, maxLength }
+  return {
+    value: {
+      length,
+      refSeqId,
+      refSeqStart,
+      alignmentSpan,
+      numBlocks,
+      numLandmarks,
+      numBases,
+      recordCounter,
+      numRecords,
+    },
+    maxLength,
+    offset,
+  }
+}
+
+function getCramContainerHeader2(
+  majorVersion: number,
+  buffer: Buffer,
+  dataView: DataView,
+  offset: number,
+) {
+  const [numLandmarks, newOffset1] = parseItf8(buffer, offset)
+  offset += newOffset1
+  const landmarks = []
+  for (let i = 0; i < numLandmarks; i++) {
+    const [landmark, newOffset2] = parseItf8(buffer, offset)
+    offset += newOffset2
+    landmarks.push(landmark)
+  }
+
+  let crcLength = 0
+  let crc32
+  if (majorVersion >= 3) {
+    crc32 = dataView.getUint32(offset)
+    crcLength = 4
+  }
+  return {
+    value: {
+      crc32,
+      numLandmarks,
+      landmarks,
+    },
+    maxLength: 5 + numLandmarks * 5 + crcLength,
+    offset,
+  }
 }
 
 // each of these is a function of the major and minor version
@@ -689,57 +729,8 @@ const versionedParsers = {
   getCramDataSeriesEncodingMap,
   getCramTagEncodingMap,
   getCramCompressionHeader,
-
-  cramContainerHeader1(majorVersion: number) {
-    let parser = new Parser()
-      .int32('length') // byte size of the container data (blocks)
-      .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
-      .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
-      .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
-      .itf8('numRecords') // number of records in the container
-    let maxLength = 4 + 5 * 4
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter') // 1-based sequential index of records in the file/stream.
-      maxLength += 9
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter')
-      maxLength += 5
-    }
-
-    if (majorVersion > 1) {
-      parser = parser.ltf8('numBases') // number of read bases
-      maxLength += 9
-    }
-    parser = parser
-      .itf8('numBlocks') // the number of blocks
-      .itf8('numLandmarks') // the number of landmarks
-    maxLength += 5 + 5
-
-    return { parser, maxLength }
-  },
-
-  cramContainerHeader2(majorVersion: number) {
-    let parser = new Parser()
-      .itf8('numLandmarks') // the number of blocks
-      // Each integer value of this array is a byte offset
-      // into the blocks byte array. Landmarks are used for
-      // random access indexing.
-      .array('landmarks', {
-        type: new Parser().itf8(),
-        length: 'numLandmarks',
-      })
-
-    let crcLength = 0
-    if (majorVersion >= 3) {
-      parser = parser.uint32('crc32')
-      crcLength = 4
-    }
-    return {
-      parser,
-      maxLength: (numLandmarks: number) => 5 + numLandmarks * 5 + crcLength,
-    }
-  },
+  getCramContainerHeader1,
+  getCramContainerHeader2,
 }
 
 export type CompressionMethod =

yarn.lock

@@ -336,13 +336,6 @@
     long "^4.0.0"
     pako "^1.0.11"
 
-"@gmod/binary-parser@^1.3.5":
-  version "1.4.2"
-  resolved "https://registry.yarnpkg.com/@gmod/binary-parser/-/binary-parser-1.4.2.tgz#54f50e7b3437cc0882bd8ba6ef7c8e664ae3e892"
-  integrity sha512-X/UI86z2l6+qhy3Biai9Mog5/PPT3HR8+xo6qALijQ6FpRovkd/OPWOgy2fZX3vMRuMcyZKUva7V24Iir8HfhQ==
-  dependencies:
-    long "^4.0.0"
-
 "@gmod/indexedfasta@^2.1.0":
   version "2.1.1"
   resolved "https://registry.yarnpkg.com/@gmod/indexedfasta/-/indexedfasta-2.1.1.tgz#aa8eaf6be21f634f11da90dd8494f3df5ed7e50d"