@gmod/bam 1.1.18 → 2.0.1

package/src/record.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-empty-function */
 import Constants from './constants'
 
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('')
@@ -83,11 +82,11 @@ export default class BamRecord {
     }
     tags = tags.concat(this._tagList || [])
 
-    Object.keys(this.data).forEach(k => {
+    for (const k of Object.keys(this.data)) {
       if (k[0] !== '_' && k !== 'next_seq_id') {
         tags.push(k)
       }
-    })
+    }
 
     const seen: { [key: string]: boolean } = {}
     return tags.filter(t => {
@@ -107,7 +106,7 @@ export default class BamRecord {
   }
 
   parent() {
-    return undefined
+    return
   }
 
   children() {
@@ -137,7 +136,7 @@ export default class BamRecord {
 
   qualRaw() {
     if (this.isSegmentUnmapped()) {
-      return undefined
+      return
     }
 
     const { start, byteArray } = this.bytes
@@ -157,7 +156,7 @@ export default class BamRecord {
 
   multi_segment_next_segment_strand() {
     if (this.isMateUnmapped()) {
-      return undefined
+      return
     }
     return this.isMateReverseComplemented() ? -1 : 1
   }
@@ -181,7 +180,7 @@ export default class BamRecord {
     // called, we already know that we have no such tag, because
     // it would already have been cached.
     if (this._allTagsParsed) {
-      return undefined
+      return
     }
 
     const { byteArray, start } = this.bytes
@@ -204,40 +203,48 @@ export default class BamRecord {
 
       let value
       switch (type) {
-        case 'A':
+        case 'A': {
           value = String.fromCharCode(byteArray[p])
           p += 1
           break
-        case 'i':
+        }
+        case 'i': {
           value = byteArray.readInt32LE(p)
           p += 4
           break
-        case 'I':
+        }
+        case 'I': {
           value = byteArray.readUInt32LE(p)
           p += 4
           break
-        case 'c':
+        }
+        case 'c': {
           value = byteArray.readInt8(p)
           p += 1
           break
-        case 'C':
+        }
+        case 'C': {
           value = byteArray.readUInt8(p)
           p += 1
           break
-        case 's':
+        }
+        case 's': {
           value = byteArray.readInt16LE(p)
           p += 2
           break
-        case 'S':
+        }
+        case 'S': {
           value = byteArray.readUInt16LE(p)
           p += 2
           break
-        case 'f':
+        }
+        case 'f': {
           value = byteArray.readFloatLE(p)
           p += 4
           break
+        }
         case 'Z':
-        case 'H':
+        case 'H': {
           value = ''
           while (p <= blockEnd) {
             const cc = byteArray[p++]
@@ -248,6 +255,7 @@ export default class BamRecord {
             }
           }
           break
+        }
         case 'B': {
           value = ''
           const cc = byteArray[p++]
@@ -339,10 +347,11 @@ export default class BamRecord {
           }
           break
         }
-        default:
+        default: {
           console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`)
           value = undefined
-          p = blockEnd // stop parsing tags
+          p = blockEnd
+        } // stop parsing tags
       }
 
       this._tagOffset = p
@@ -355,7 +364,7 @@ export default class BamRecord {
       this.data[lcTag] = value
     }
     this._allTagsParsed = true
-    return undefined
+    return
   }
 
   _parseAllTags() {
@@ -368,7 +377,7 @@ export default class BamRecord {
       cigar
         .match(/\d+\D/g)
         //@ts-ignore
-        .map(op => [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)])
+        .map(op => [op.match(/\D/)[0].toUpperCase(), Number.parseInt(op, 10)])
     )
   }
 
@@ -436,7 +445,7 @@ export default class BamRecord {
 
   cigar() {
     if (this.isSegmentUnmapped()) {
-      return undefined
+      return
     }
 
     const { byteArray, start } = this.bytes
@@ -568,7 +577,7 @@ export default class BamRecord {
       }
       return tmp.join('')
     }
-    return null
+    return ''
   }
 
   _bin_mq_nl() {
@@ -597,13 +606,13 @@ export default class BamRecord {
 
   toJSON() {
     const data: { [key: string]: any } = {}
-    Object.keys(this).forEach(k => {
+    for (const k of Object.keys(this)) {
       if (k.charAt(0) === '_' || k === 'bytes') {
-        return
+        continue
       }
       //@ts-ignore
       data[k] = this[k]
-    })
+    }
 
     return data
   }

package/src/sam.ts

@@ -1,15 +1,19 @@
 export function parseHeaderText(text: string) {
   const lines = text.split(/\r?\n/)
   const data: { tag: string; data: { tag: string; value: string }[] }[] = []
-  lines.forEach(line => {
+  for (const line of lines) {
     const [tag, ...fields] = line.split(/\t/)
-    const parsedFields = fields.map(f => {
-      const [fieldTag, value] = f.split(':', 2)
-      return { tag: fieldTag, value }
-    })
     if (tag) {
-      data.push({ tag: tag.substr(1), data: parsedFields })
+      data.push({
+        tag: tag.slice(1),
+        data: fields.map(f => {
+          const r = f.indexOf(':')
+          const fieldTag = f.slice(0, r)
+          const value = f.slice(r + 1)
+          return { tag: fieldTag, value }
+        }),
+      })
     }
-  })
+  }
   return data
 }

package/src/util.ts

@@ -1,3 +1,4 @@
+import Long from 'long'
 import Chunk from './chunk'
 import VirtualOffset from './virtualOffset'
 
@@ -33,13 +34,13 @@ export function checkAbortSignal(signal?: AbortSignal) {
 
   if (signal.aborted) {
     // console.log('bam aborted!')
-    if (typeof DOMException !== 'undefined') {
-      throw new DOMException('aborted', 'AbortError')
-    } else {
+    if (typeof DOMException === 'undefined') {
       const e = new Error('aborted')
       //@ts-ignore
       e.code = 'ERR_ABORTED'
       throw e
+    } else {
+      throw new DOMException('aborted', 'AbortError')
     }
   }
 }
@@ -77,9 +78,9 @@ export function makeOpts(obj: AbortSignal | BaseOpts = {}): BaseOpts {
   return 'aborted' in obj ? ({ signal: obj } as BaseOpts) : (obj as BaseOpts)
 }
 
-export function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset) {
+export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
   const mergedChunks: Chunk[] = []
-  let lastChunk: Chunk | null = null
+  let lastChunk: Chunk | undefined
 
   if (chunks.length === 0) {
     return chunks
@@ -87,16 +88,12 @@ export function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset) {
 
   chunks.sort((c0, c1) => {
     const dif = c0.minv.blockPosition - c1.minv.blockPosition
-    if (dif !== 0) {
-      return dif
-    } else {
-      return c0.minv.dataPosition - c1.minv.dataPosition
-    }
+    return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif
   })
 
-  chunks.forEach(chunk => {
+  for (const chunk of chunks) {
     if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-      if (lastChunk === null) {
+      if (lastChunk === undefined) {
         mergedChunks.push(chunk)
         lastChunk = chunk
       } else {
@@ -110,7 +107,51 @@ export function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset) {
         }
       }
     }
-  })
+  }
 
   return mergedChunks
 }
+
+export function parsePseudoBin(bytes: Buffer, offset: number) {
+  const lineCount = longToNumber(
+    Long.fromBytesLE(
+      Array.prototype.slice.call(bytes, offset, offset + 8),
+      true,
+    ),
+  )
+  return { lineCount }
+}
+
+export function findFirstData(
+  firstDataLine: VirtualOffset | undefined,
+  virtualOffset: VirtualOffset,
+) {
+  return firstDataLine
+    ? firstDataLine.compareTo(virtualOffset) > 0
+      ? virtualOffset
+      : firstDataLine
+    : virtualOffset
+}
+
+export function parseNameBytes(
+  namesBytes: Buffer,
+  renameRefSeq: (arg: string) => string = s => s,
+) {
+  let currRefId = 0
+  let currNameStart = 0
+  const refIdToName = []
+  const refNameToId: { [key: string]: number } = {}
+  for (let i = 0; i < namesBytes.length; i += 1) {
+    if (!namesBytes[i]) {
+      if (currNameStart < i) {
+        let refName = namesBytes.toString('utf8', currNameStart, i)
+        refName = renameRefSeq(refName)
+        refIdToName[currRefId] = refName
+        refNameToId[refName] = currRefId
+      }
+      currNameStart = i + 1
+      currRefId += 1
+    }
+  }
+  return { refNameToId, refIdToName }
+}

package/src/declare.d.ts

@@ -1,2 +0,0 @@
-declare module 'object.entries-ponyfill'
-declare module '@gmod/bgzf-filehandle'