@gmod/cram 4.0.10 → 5.0.0

package/src/cramFile/file.ts

@@ -2,22 +2,22 @@ import crc32 from 'crc/calculators/crc32'
 import QuickLRU from 'quick-lru'
 import { XzReadableStream } from 'xz-decompress'
 
-import { CramMalformedError, CramUnimplementedError } from '../errors'
-import * as htscodecs from '../htscodecs'
-import { open } from '../io'
-import ransuncompress from '../rans'
-import { parseHeaderText } from '../sam'
-import { decode } from '../seek-bzip'
-import { unzip } from '../unzip'
-import CramContainer from './container'
-import CramRecord from './record'
+import { CramMalformedError, CramUnimplementedError } from '../errors.ts'
+import * as htscodecs from '../htscodecs/index.ts'
+import { open } from '../io.ts'
+import ransuncompress from '../rans/index.ts'
+import { parseHeaderText } from '../sam.ts'
+import { decode } from '../seek-bzip/index.ts'
+import { unzip } from '../unzip.ts'
+import CramContainer from './container/index.ts'
+import CramRecord from './record.ts'
 import {
   BlockHeader,
   CompressionMethod,
   cramFileDefinition,
   getSectionParsers,
-} from './sectionParsers'
-import { parseItem, tinyMemoize } from './util'
+} from './sectionParsers.ts'
+import { parseItem, tinyMemoize } from './util.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 
@@ -282,11 +282,7 @@ export default class CramFile {
   ) {
     // console.log({ compressionMethod })
     if (compressionMethod === 'gzip') {
-      const ret = unzip(inputBuffer)
-      if (ret[0] === 24) {
-        // console.log(ret.slice(0, 500).join(','))
-      }
-      return ret
+      return unzip(inputBuffer)
     } else if (compressionMethod === 'bzip2') {
       return decode(inputBuffer)
     } else if (compressionMethod === 'lzma') {
@@ -298,8 +294,6 @@ export default class CramFile {
       const outputBuffer = new Uint8Array(uncompressedSize)
       ransuncompress(inputBuffer, outputBuffer)
       return outputBuffer
-      // htscodecs r4x8 is slower, but compatible.
-      // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
     } else if (compressionMethod === 'rans4x16') {
       return htscodecs.r4x16_uncompress(inputBuffer)
     } else if (compressionMethod === 'arith') {

package/src/cramFile/index.ts

@@ -1,3 +1,3 @@
-export { default as CramRecord } from './record'
+export { default as CramRecord } from './record.ts'
 
-export { default } from './file'
+export { default } from './file.ts'

package/src/cramFile/record.ts

@@ -1,7 +1,7 @@
-import Constants from './constants'
-import CramContainerCompressionScheme from './container/compressionScheme'
+import Constants from './constants.ts'
+import CramContainerCompressionScheme from './container/compressionScheme.ts'
 
-import type decodeRecord from './slice/decodeRecord'
+import type decodeRecord from './slice/decodeRecord.ts'
 
 export interface RefRegion {
   start: number

package/src/cramFile/sectionParsers.ts

@@ -1,7 +1,7 @@
-import { TupleOf } from '../typescript'
-import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes'
-import { CramEncoding } from './encoding'
-import { parseItf8, parseLtf8 } from './util'
+import { TupleOf } from '../typescript.ts'
+import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes.ts'
+import { CramEncoding } from './encoding.ts'
+import { parseItf8, parseLtf8 } from './util.ts'
 
 export function cramFileDefinition() {
   return {

package/src/cramFile/slice/decodeRecord.ts

@@ -1,18 +1,18 @@
-import { CramMalformedError } from '../../errors'
-import { Cursors, DataTypeMapping } from '../codecs/_base'
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
+import { CramMalformedError } from '../../errors.ts'
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts'
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts'
 import CramContainerCompressionScheme, {
   DataSeriesTypes,
-} from '../container/compressionScheme'
+} from '../container/compressionScheme.ts'
 import {
   BamFlagsDecoder,
   CramFlagsDecoder,
   MateFlagsDecoder,
   ReadFeature,
-} from '../record'
-import CramSlice, { SliceHeader } from './index'
-import { CramFileBlock } from '../file'
-import { isMappedSliceHeader } from '../sectionParsers'
+} from '../record.ts'
+import CramSlice, { SliceHeader } from './index.ts'
+import { CramFileBlock } from '../file.ts'
+import { isMappedSliceHeader } from '../sectionParsers.ts'
 
 /**
  * given a Buffer, read a string up to the first null character

package/src/cramFile/slice/index.ts

@@ -1,20 +1,20 @@
-import { CramArgumentError, CramMalformedError } from '../../errors'
-import { Cursors, DataTypeMapping } from '../codecs/_base'
-import { CramBufferOverrunError } from '../codecs/getBits'
-import Constants from '../constants'
-import decodeRecord, { DataSeriesDecoder } from './decodeRecord'
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
-import CramContainer from '../container'
-import { DataSeriesTypes } from '../container/compressionScheme'
-import CramFile, { CramFileBlock } from '../file'
-import CramRecord from '../record'
+import { CramArgumentError, CramMalformedError } from '../../errors.ts'
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts'
+import { CramBufferOverrunError } from '../codecs/getBits.ts'
+import Constants from '../constants.ts'
+import decodeRecord, { DataSeriesDecoder } from './decodeRecord.ts'
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts'
+import { DataSeriesTypes } from '../container/compressionScheme.ts'
+import CramContainer from '../container/index.ts'
+import CramFile, { CramFileBlock } from '../file.ts'
+import CramRecord from '../record.ts'
 import {
   MappedSliceHeader,
   UnmappedSliceHeader,
   getSectionParsers,
   isMappedSliceHeader,
-} from '../sectionParsers'
-import { parseItem, sequenceMD5, tinyMemoize } from '../util'
+} from '../sectionParsers.ts'
+import { parseItem, sequenceMD5, tinyMemoize } from '../util.ts'
 
 export type SliceHeader = CramFileBlock & {
   parsedContent: MappedSliceHeader | UnmappedSliceHeader
@@ -28,15 +28,12 @@ interface RefRegion {
 }
 
 /**
- * @private
- * Try to estimate the template length from a bunch of interrelated multi-segment reads.
- * @param {Array[CramRecord]} allRecords
- * @param {number} currentRecordNumber
- * @param {CramRecord} thisRecord
+ * Try to estimate the template length from a bunch of interrelated
+ * multi-segment reads.
  */
 function calculateMultiSegmentMatedTemplateLength(
   allRecords: CramRecord[],
-  currentRecordNumber: number,
+  _currentRecordNumber: number,
   thisRecord: CramRecord,
 ) {
   function getAllMatedRecords(startRecord: CramRecord) {
@@ -73,18 +70,16 @@ function calculateMultiSegmentMatedTemplateLength(
 }
 
 /**
- * @private
- * Attempt to calculate the `templateLength` for a pair of intra-slice paired reads.
- * Ported from htslib. Algorithm is imperfect.
- * @param {CramRecord} thisRecord
- * @param {CramRecord} mateRecord
+ * Attempt to calculate the `templateLength` for a pair of intra-slice paired
+ * reads. Ported from htslib. Algorithm is imperfect.
  */
 function calculateIntraSliceMatePairTemplateLength(
   thisRecord: CramRecord,
   mateRecord: CramRecord,
 ) {
-  // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-  // read, because gapping in the alignment doesn't mean the template is longer or shorter
+  // this just estimates the template length by using the simple (non-gapped)
+  // end coordinate of each read, because gapping in the alignment doesn't mean
+  // the template is longer or shorter
   const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart)
   const end = Math.max(
     thisRecord.alignmentStart + thisRecord.readLength - 1,
@@ -96,10 +91,9 @@ function calculateIntraSliceMatePairTemplateLength(
 }
 
 /**
- * @private establishes a mate-pair relationship between two records in the
- * same slice. CRAM compresses mate-pair relationships between records in the
- * same slice down into just one record having the index in the slice of its
- * mate
+ * establishes a mate-pair relationship between two records in the same slice.
+ * CRAM compresses mate-pair relationships between records in the same slice
+ * down into just one record having the index in the slice of its mate
  */
 function associateIntraSliceMate(
   allRecords: CramRecord[],

package/src/htscodecs/arith_gen.ts

@@ -34,12 +34,12 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import { decode } from '../seek-bzip'
+import { decode } from '../seek-bzip/index.ts'
 
-import RangeCoder from './arith_sh'
-import ByteModel from './byte_model'
-import IOStream from './iostream'
-import { concatUint8Array } from '../util'
+import RangeCoder from './arith_sh.ts'
+import ByteModel from './byte_model.ts'
+import IOStream from './iostream.ts'
+import { concatUint8Array } from '../util.ts'
 
 const ARITH_ORDER = 1
 const ARITH_EXT = 4

package/src/htscodecs/fqzcomp.ts

@@ -34,9 +34,9 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import RangeCoder from './arith_sh'
-import ByteModel from './byte_model'
-import IOStream from './iostream'
+import RangeCoder from './arith_sh.ts'
+import ByteModel from './byte_model.ts'
+import IOStream from './iostream.ts'
 
 // ----------------------------------------------------------------------
 // Main arithmetic entry function: decodes a compressed src and

package/src/htscodecs/index.ts

@@ -39,11 +39,11 @@
 // This JavaScript file is not part of the reference implementation
 // and is simply and interface to get a consistent interface for cram-js.
 
-import arith from './arith_gen'
-import * as fqzcomp from './fqzcomp'
-import * as r4x8 from './rans'
-import * as r4x16 from './rans4x16'
-import * as tok3 from './tok3'
+import arith from './arith_gen.ts'
+import * as fqzcomp from './fqzcomp.ts'
+import * as r4x8 from './rans.ts'
+import * as r4x16 from './rans4x16.ts'
+import * as tok3 from './tok3.ts'
 
 export function r4x8_uncompress(inputBuffer: Uint8Array) {
   return r4x8.decode(inputBuffer)

package/src/htscodecs/rans.ts

@@ -34,7 +34,7 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import IOStream from './iostream'
+import IOStream from './iostream.ts'
 
 // ----------------------------------------------------------------------
 // rANS primitives itself

package/src/htscodecs/rans4x16.ts

@@ -34,7 +34,7 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import IOStream from './iostream'
+import IOStream from './iostream.ts'
 
 // ----------------------------------------------------------------------
 // rANS primitives itself

package/src/htscodecs/tok3.ts

@@ -40,10 +40,10 @@
 // written specification as closely as possible.  It is *NOT*
 // an efficient implementation, but see comments below.
 
-import { concatUint8Array } from '../util'
-import arith_gen from './arith_gen'
-import IOStream from './iostream'
-import * as rans from './rans4x16'
+import { concatUint8Array } from '../util.ts'
+import arith_gen from './arith_gen.ts'
+import IOStream from './iostream.ts'
+import * as rans from './rans4x16.ts'
 
 const arith = new arith_gen()
 

package/src/index.ts

@@ -1,3 +1,3 @@
-export { CramRecord, default as CramFile } from './cramFile'
-export { default as CraiIndex } from './craiIndex'
-export { default as IndexedCramFile } from './indexedCramFile'
+export { CramRecord, default as CramFile } from './cramFile/index.ts'
+export { default as CraiIndex } from './craiIndex.ts'
+export { default as IndexedCramFile } from './indexedCramFile.ts'

package/src/indexedCramFile.ts

@@ -1,8 +1,8 @@
-import { Slice } from './craiIndex'
-import CramFile from './cramFile'
-import { SeqFetch } from './cramFile/file'
-import CramRecord from './cramFile/record'
-import { CramUnimplementedError } from './errors'
+import { Slice } from './craiIndex.ts'
+import { SeqFetch } from './cramFile/file.ts'
+import CramFile from './cramFile/index.ts'
+import CramRecord from './cramFile/record.ts'
+import { CramUnimplementedError } from './errors.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 

package/src/rans/d04.ts

@@ -1,7 +1,7 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors'
-import { TF_SHIFT } from './constants'
-import Decoding from './decoding'
+import { CramMalformedError } from '../errors.ts'
+import { TF_SHIFT } from './constants.ts'
+import Decoding from './decoding.ts'
 
 export default function uncompress(
   /* ByteBuffer */ input,

package/src/rans/d14.ts

@@ -1,6 +1,6 @@
 // @ts-nocheck
-import { TF_SHIFT } from './constants'
-import Decoding from './decoding'
+import { TF_SHIFT } from './constants.ts'
+import Decoding from './decoding.ts'
 
 export default function uncompress(
   /* ByteBuffer */ input,

package/src/rans/decoding.ts

@@ -1,6 +1,6 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors'
-import { RANS_BYTE_L } from './constants'
+import { CramMalformedError } from '../errors.ts'
+import { RANS_BYTE_L } from './constants.ts'
 
 class FC {
   // int F, C;

package/src/rans/frequencies.ts

@@ -1,7 +1,7 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors'
-import { TOTFREQ } from './constants'
-import Decoding from './decoding'
+import { CramMalformedError } from '../errors.ts'
+import { TOTFREQ } from './constants.ts'
+import Decoding from './decoding.ts'
 
 function assert(result) {
   if (!result) {

package/src/rans/index.ts

@@ -1,9 +1,9 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors'
-import D04 from './d04'
-import D14 from './d14'
-import Decoding from './decoding'
-import { readStatsO0, readStatsO1 } from './frequencies'
+import { CramMalformedError } from '../errors.ts'
+import D04 from './d04.ts'
+import D14 from './d14.ts'
+import Decoding from './decoding.ts'
+import { readStatsO0, readStatsO1 } from './frequencies.ts'
 
 // const /* int */ ORDER_BYTE_LENGTH = 1
 // const /* int */ COMPRESSED_BYTE_LENGTH = 4

package/dist/cram-bundle.js.LICENSE.txt

@@ -1,12 +0,0 @@
-/*!
- * Based on xzwasm (c) Steve Sanderson. License: MIT - https://github.com/SteveSanderson/xzwasm
- * Contains xz-embedded by Lasse Collin and Igor Pavlov. License: Public domain - https://tukaani.org/xz/embedded.html
- * and walloc (c) 2020 Igalia, S.L. License: MIT - https://github.com/wingo/walloc
- */
-
-/*!
- * Determine if an object is a Buffer
- *
- * @author   Feross Aboukhadijeh <https://feross.org>
- * @license  MIT
- */

package/dist/io/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;AAqBS,oBAAI;AArBb,6DAA2D;AAI3D,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAAmC;IAEnC,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,IAAI,gCAAU,CAAC,QAAQ,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,+BAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAID,2DAA2D;AAAlD,gHAAA,SAAS,OAAA;AAAE,iHAAA,UAAU,OAAA"}

package/esm/io/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAI3D,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAAmC;IAEnC,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,IAAI,UAAU,CAAC,QAAQ,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,SAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,IAAI,EAAE,CAAA;AAEf,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA"}

package/src/cramFile/declare.d.ts

@@ -1 +0,0 @@
-declare module 'seek-bzip'