@gmod/cram 1.5.9 → 1.6.2

package/src/cramFile/slice/decodeRecord.js

@@ -0,0 +1,362 @@
+import Long from 'long'
+import { CramMalformedError, CramUnimplementedError } from '../../errors'
+import CramRecord from '../record'
+import Constants from '../constants'
+/**
+ * given a Buffer, read a string up to the first null character
+ * @private
+ */
+function readNullTerminatedStringFromBuffer(buffer) {
+  const zeroOffset = buffer.indexOf(0)
+  if (zeroOffset === -1) {
+    return buffer.toString('utf8')
+  }
+  return buffer.toString('utf8', 0, zeroOffset)
+}
+
+/**
+ * parse a BAM tag's array value from a binary buffer
+ * @private
+ */
+function parseTagValueArray(buffer) {
+  const arrayType = String.fromCharCode(buffer[0])
+  const length = buffer.readInt32LE(1)
+
+  const schema = {
+    c: ['readInt8', 1],
+    C: ['readUInt8', 1],
+    s: ['readInt16LE', 2],
+    S: ['readUInt16LE', 2],
+    i: ['readInt32LE', 4],
+    I: ['readUInt32LE', 4],
+    f: ['readFloatLE', 4],
+  }[arrayType]
+  if (!schema) {
+    throw new CramMalformedError(`invalid tag value array type '${arrayType}'`)
+  }
+
+  const [getMethod, itemSize] = schema
+  const array = new Array(length)
+  let offset = 5
+  for (let i = 0; i < length; i += 1) {
+    array[i] = buffer[getMethod](offset)
+    offset += itemSize
+  }
+  return array
+}
+
+function parseTagData(tagType, buffer) {
+  if (!buffer.readInt32LE) {
+    buffer = Buffer.from(buffer)
+  }
+  if (tagType === 'Z') {
+    return readNullTerminatedStringFromBuffer(buffer)
+  }
+  if (tagType === 'A') {
+    return String.fromCharCode(buffer[0])
+  }
+  if (tagType === 'I') {
+    const val = Long.fromBytesLE(buffer)
+    if (
+      val.greaterThan(Number.MAX_SAFE_INTEGER) ||
+      val.lessThan(Number.MIN_SAFE_INTEGER)
+    ) {
+      throw new CramUnimplementedError('integer overflow')
+    }
+    return val.toNumber()
+  }
+  if (tagType === 'i') {
+    return buffer.readInt32LE(0)
+  }
+  if (tagType === 's') {
+    return buffer.readInt16LE(0)
+  }
+  if (tagType === 'S') {
+    return buffer.readUInt16LE(0)
+  }
+  if (tagType === 'c') {
+    return buffer.readInt8(0)
+  }
+  if (tagType === 'C') {
+    return buffer.readUInt8(0)
+  }
+  if (tagType === 'f') {
+    return buffer.readFloatLE(0)
+  }
+  if (tagType === 'H') {
+    const hex = readNullTerminatedStringFromBuffer(buffer)
+    return Number.parseInt(hex.replace(/^0x/, ''), 16)
+  }
+  if (tagType === 'B') {
+    return parseTagValueArray(buffer)
+  }
+
+  throw new CramMalformedError(`Unrecognized tag type ${tagType}`)
+}
+
+function decodeReadFeatures(
+  cramRecord,
+  readFeatureCount,
+  decodeDataSeries,
+  compressionScheme,
+  majorVersion,
+) {
+  let currentReadPos = 0
+  let currentRefPos = cramRecord.alignmentStart - 1
+  const readFeatures = new Array(readFeatureCount)
+
+  function decodeRFData([type, dataSeriesName]) {
+    const data = decodeDataSeries(dataSeriesName)
+    if (type === 'character') {
+      return String.fromCharCode(data)
+    }
+    if (type === 'string') {
+      return data.toString('utf8')
+    }
+    if (type === 'numArray') {
+      return data.toArray()
+    }
+    // else if (type === 'number') {
+    //   return data[0]
+    // }
+    return data
+  }
+
+  for (let i = 0; i < readFeatureCount; i += 1) {
+    const code = String.fromCharCode(decodeDataSeries('FC'))
+
+    const readPosDelta = decodeDataSeries('FP')
+
+    const readFeature = { code }
+    // map of operator name -> data series name
+    const data1Schema = {
+      B: ['character', 'BA'],
+      S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
+      X: ['number', 'BS'],
+      D: ['number', 'DL'],
+      I: ['string', 'IN'],
+      i: ['character', 'BA'],
+      b: ['string', 'BB'],
+      q: ['numArray', 'QQ'],
+      Q: ['number', 'QS'],
+      H: ['number', 'HC'],
+      P: ['number', 'PD'],
+      N: ['number', 'RS'],
+    }[code]
+
+    if (!data1Schema) {
+      throw new CramMalformedError(`invalid read feature code "${code}"`)
+    }
+
+    readFeature.data = decodeRFData(data1Schema)
+
+    // if this is a tag with two data items, make the data an array and add the second item
+    const data2Schema = { B: ['number', 'QS'] }[code]
+    if (data2Schema) {
+      readFeature.data = [readFeature.data, decodeRFData(data2Schema)]
+    }
+
+    currentReadPos += readPosDelta
+    readFeature.pos = currentReadPos
+
+    currentRefPos += readPosDelta
+    readFeature.refPos = currentRefPos
+
+    // for gapping features, adjust the reference position for read features that follow
+    if (code === 'D' || code === 'N') {
+      currentRefPos += readFeature.data
+    } else if (code === 'I' || code === 'S') {
+      currentRefPos -= readFeature.data.length
+    } else if (code === 'i') {
+      currentRefPos -= 1
+    }
+
+    readFeatures[i] = readFeature
+  }
+  return readFeatures
+}
+
+function thingToString(thing) {
+  if (thing instanceof Buffer) {
+    return readNullTerminatedStringFromBuffer(thing)
+  }
+  if (thing.length && thing.indexOf) {
+    // array-like
+    if (!thing[thing.length - 1]) {
+      // trim zeroes off the end if necessary
+      const termIndex = thing.indexOf(0)
+      return String.fromCharCode(...thing.slice(0, termIndex))
+    }
+    return String.fromCharCode(...thing)
+  }
+  return String(thing)
+}
+
+export default function decodeRecord(
+  slice,
+  decodeDataSeries,
+  compressionScheme,
+  sliceHeader,
+  coreDataBlock,
+  blocksByContentId,
+  cursors,
+  majorVersion,
+  recordNumber,
+) {
+  const cramRecord = new CramRecord()
+
+  cramRecord.flags = decodeDataSeries('BF')
+
+  // note: the C data type of compressionFlags is byte in cram v1
+  // and int32 in cram v2+, but that does not matter for us here
+  // in javascript land.
+  cramRecord.cramFlags = decodeDataSeries('CF')
+
+  if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) {
+    cramRecord.sequenceId = decodeDataSeries('RI')
+  } else {
+    cramRecord.sequenceId = sliceHeader.content.refSeqId
+  }
+
+  cramRecord.readLength = decodeDataSeries('RL')
+  // if APDelta, will calculate the true start in a second pass
+  cramRecord.alignmentStart = decodeDataSeries('AP')
+  if (compressionScheme.APdelta) {
+    cramRecord.alignmentStart += cursors.lastAlignmentStart
+  }
+  cursors.lastAlignmentStart = cramRecord.alignmentStart
+  cramRecord.readGroupId = decodeDataSeries('RG')
+
+  if (compressionScheme.readNamesIncluded) {
+    cramRecord.readName = thingToString(decodeDataSeries('RN'))
+  }
+
+  // mate record
+  if (cramRecord.isDetached()) {
+    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
+    const mate = {}
+    mate.flags = decodeDataSeries('MF')
+    if (!compressionScheme.readNamesIncluded) {
+      mate.readName = thingToString(decodeDataSeries('RN'))
+      cramRecord.readName = mate.readName
+    }
+    mate.sequenceId = decodeDataSeries('NS')
+    mate.alignmentStart = decodeDataSeries('NP')
+    if (mate.flags || mate.sequenceId > -1) {
+      cramRecord.mate = mate
+    }
+    cramRecord.templateSize = decodeDataSeries('TS')
+
+    // set mate unmapped if needed
+    if (mate.flags & Constants.CRAM_M_UNMAP) {
+      cramRecord.flags |= Constants.BAM_FMUNMAP
+    }
+    // set mate reversed if needed
+    if (mate.flags & Constants.CRAM_M_REVERSE) {
+      cramRecord.flags |= Constants.BAM_FMREVERSE
+    }
+
+    // detachedCount++
+  } else if (cramRecord.hasMateDownStream()) {
+    cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1
+  }
+
+  // TODO: the aux tag parsing will have to be refactored if we want to support
+  // cram v1
+  const TLindex = decodeDataSeries('TL')
+  if (TLindex < 0) {
+    /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
+    throw new CramMalformedError('invalid TL index')
+  }
+
+  // TN = tag names
+  const TN = compressionScheme.getTagNames(TLindex)
+  const ntags = TN.length
+
+  for (let i = 0; i < ntags; i += 1) {
+    const tagId = TN[i]
+    const tagName = tagId.substr(0, 2)
+    const tagType = tagId.substr(2, 1)
+
+    const tagCodec = compressionScheme.getCodecForTag(tagId)
+    if (!tagCodec) {
+      throw new CramMalformedError(
+        `no codec defined for auxiliary tag ${tagId}`,
+      )
+    }
+    const tagData = tagCodec.decode(
+      slice,
+      coreDataBlock,
+      blocksByContentId,
+      cursors,
+    )
+    cramRecord.tags[tagName] = parseTagData(tagType, tagData)
+  }
+
+  if (!cramRecord.isSegmentUnmapped()) {
+    // reading read features
+    const /* int */ readFeatureCount = decodeDataSeries('FN')
+    if (readFeatureCount) {
+      cramRecord.readFeatures = decodeReadFeatures(
+        cramRecord,
+        readFeatureCount,
+        decodeDataSeries,
+        compressionScheme,
+        majorVersion,
+      )
+    }
+
+    // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+    let lengthOnRef = cramRecord.readLength
+    if (cramRecord.readFeatures) {
+      cramRecord.readFeatures.forEach(({ code, data }) => {
+        if (code === 'D' || code === 'N') {
+          lengthOnRef += data
+        } else if (code === 'I' || code === 'S') {
+          lengthOnRef -= data.length
+        } else if (code === 'i') {
+          lengthOnRef -= 1
+        }
+      })
+    }
+    if (Number.isNaN(lengthOnRef)) {
+      console.warn(
+        `${
+          cramRecord.readName ||
+          `${cramRecord.sequenceId}:${cramRecord.alignmentStart}`
+        } record has invalid read features`,
+      )
+      lengthOnRef = cramRecord.readLength
+    }
+    cramRecord.lengthOnRef = lengthOnRef
+
+    // mapping quality
+    cramRecord.mappingQuality = decodeDataSeries('MQ')
+    if (cramRecord.isPreservingQualityScores()) {
+      const bases = new Array(cramRecord.readLength)
+      for (let i = 0; i < bases.length; i += 1) {
+        bases[i] = decodeDataSeries('QS')
+      }
+      cramRecord.qualityScores = bases
+    }
+  } else if (cramRecord.isUnknownBases()) {
+    cramRecord.readBases = null
+    cramRecord.qualityScores = null
+  } else {
+    const bases = new Array(cramRecord.readLength)
+    for (let i = 0; i < bases.length; i += 1) {
+      bases[i] = decodeDataSeries('BA')
+    }
+    cramRecord.readBases = String.fromCharCode(...bases)
+
+    if (cramRecord.isPreservingQualityScores()) {
+      for (let i = 0; i < bases.length; i += 1) {
+        bases[i] = decodeDataSeries('QS')
+      }
+
+      cramRecord.qualityScores = bases
+    }
+  }
+
+  return cramRecord
+}