diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..53633b9 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,3 @@ +test/data +dist +esm diff --git a/src/cramFile/container/index.ts b/src/cramFile/container/index.ts index 7af509e..092c6e3 100644 --- a/src/cramFile/container/index.ts +++ b/src/cramFile/container/index.ts @@ -22,8 +22,8 @@ export default class CramContainer { // if there are no records in the container, there will be no compression // header - if (!containerHeader?.numRecords) { - return null + if (!containerHeader.numRecords) { + return undefined } const { majorVersion } = await this.file.getDefinition() const sectionParsers = getSectionParsers(majorVersion) @@ -52,9 +52,6 @@ export default class CramContainer { async getFirstBlock() { const containerHeader = await this.getHeader() - if (!containerHeader) { - return undefined - } return this.file.readBlock(containerHeader._endPosition) } @@ -79,12 +76,6 @@ export default class CramContainer { const { majorVersion } = await this.file.getDefinition() const sectionParsers = getSectionParsers(majorVersion) const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers - const { size: fileSize } = await this.file.stat() - - if (position >= fileSize) { - console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`) - return undefined - } // parse the container header. do it in 2 pieces because you cannot tell // how much to buffer until you read numLandmarks @@ -92,13 +83,6 @@ export default class CramContainer { await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position) const header1 = parseItem(bytes1, cramContainerHeader1.parser) const numLandmarksSize = itf8Size(header1.numLandmarks) - if (position + header1.length >= fileSize) { - // header indicates container goes beyond fileSize - console.warn( - `container at ${position} is beyond fileSize:${fileSize}, skipping`, - ) - return undefined - } const bytes2 = Buffer.allocUnsafe( cramContainerHeader2.maxLength(header1.numLandmarks), ) diff --git a/src/cramFile/file.ts b/src/cramFile/file.ts index 49bd89f..4d5e69e 100644 --- a/src/cramFile/file.ts +++ b/src/cramFile/file.ts @@ -106,11 +106,6 @@ export default class CramFile { return this.file.read(buffer, offset, length, position) } - // can just stat this object like a filehandle - stat() { - return this.file.stat() - } - // memoized async getDefinition() { const { maxLength, parser } = cramFileDefinition() @@ -153,25 +148,13 @@ export default class CramFile { const { majorVersion } = await this.getDefinition() const sectionParsers = getSectionParsers(majorVersion) let position = sectionParsers.cramFileDefinition.maxLength - const { size: fileSize } = await this.file.stat() - const { cramContainerHeader1 } = sectionParsers // skip with a series of reads to the proper container let currentContainer: CramContainer | undefined for (let i = 0; i <= containerNumber; i++) { - // if we are about to go off the end of the file - // and have not found that container, it does not exist - if (position + cramContainerHeader1.maxLength + 8 >= fileSize) { - return undefined - } - currentContainer = this.getContainerAtPosition(position) const currentHeader = await currentContainer.getHeader() - if (!currentHeader) { - throw new CramMalformedError( - `container ${containerNumber} not found in file`, - ) - } + // if this is the first container, read all the blocks in the container // to determine its length, because we cannot trust the container // header's given length due to a bug somewhere in htslib @@ -185,8 +168,7 @@ export default class CramFile { position = block._endPosition } } else { - // otherwise, just traverse to the next container using the container's - // length + // otherwise, just traverse to the next container using the container's length position += currentHeader._size + currentHeader.length } } @@ -213,20 +195,18 @@ export default class CramFile { /** * @returns {Promise[number]} the number of containers in the file */ - async containerCount(): Promise { + async containerCount() { const { majorVersion } = await this.getDefinition() const sectionParsers = getSectionParsers(majorVersion) - const { size: fileSize } = await this.file.stat() - const { cramContainerHeader1 } = sectionParsers let containerCount = 0 let position = sectionParsers.cramFileDefinition.maxLength - while (position + cramContainerHeader1.maxLength + 8 < fileSize) { + let i = 0 + while (i++ < 5000) { const currentHeader = await this.getContainerAtPosition(position).getHeader() - if (!currentHeader) { - break - } + // console.log({ currentHeader }, currentHeader._endPosition) + // if this is the first container, read all the blocks in the container, // because we cannot trust the container header's given length due to a // bug somewhere in htslib @@ -244,6 +224,9 @@ export default class CramFile { // length position += currentHeader._size + currentHeader.length } + if (currentHeader.refSeqId === -1) { + return containerCount + } containerCount += 1 } @@ -258,11 +241,6 @@ export default class CramFile { const { majorVersion } = await this.getDefinition() const sectionParsers = getSectionParsers(majorVersion) const { cramBlockHeader } = sectionParsers - const { size: fileSize } = await this.file.stat() - - if (position + cramBlockHeader.maxLength >= fileSize) { - return undefined - } const buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength) await this.file.read(buffer, 0, cramBlockHeader.maxLength, position) @@ -282,10 +260,6 @@ export default class CramFile { if (preReadBuffer) { buffer = preReadBuffer } else { - const { size: fileSize } = await this.file.stat() - if (position + size >= fileSize) { - return undefined - } buffer = Buffer.allocUnsafe(size) await this.file.read(buffer, 0, size, position) } @@ -348,9 +322,6 @@ export default class CramFile { const { majorVersion } = await this.getDefinition() const sectionParsers = getSectionParsers(majorVersion) const blockHeader = await this.readBlockHeader(position) - if (blockHeader === undefined) { - return undefined - } const blockContentPosition = blockHeader._endPosition const uncompressedData = Buffer.allocUnsafe(blockHeader.uncompressedSize) @@ -391,9 +362,6 @@ export default class CramFile { sectionParsers.cramBlockCrc32, blockContentPosition + blockHeader.compressedSize, ) - if (crc === undefined) { - return undefined - } block.crc32 = crc.crc32 // check the block data crc32 diff --git a/src/cramFile/record.ts b/src/cramFile/record.ts index 442f885..512408c 100644 --- a/src/cramFile/record.ts +++ b/src/cramFile/record.ts @@ -21,11 +21,11 @@ export interface ReadFeature { function decodeReadSequence(cramRecord: CramRecord, refRegion: RefRegion) { // if it has no length, it has no sequence if (!cramRecord.lengthOnRef && !cramRecord.readLength) { - return null + return undefined } if (cramRecord.isUnknownBases()) { - return null + return undefined } // remember: all coordinates are 1-based closed @@ -437,7 +437,7 @@ export default class CramRecord { } return tmp.join('') } - return null + return undefined } /** diff --git a/src/cramFile/sectionParsers.ts b/src/cramFile/sectionParsers.ts index d8dc302..e2539be 100644 --- a/src/cramFile/sectionParsers.ts +++ b/src/cramFile/sectionParsers.ts @@ -1,3 +1,4 @@ +import type { Buffer } from 'buffer' import { TupleOf } from '../typescript' import { parseItf8, parseLtf8 } from './util' import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes' @@ -92,7 +93,10 @@ export function cramBlockHeader() { }, } } - return { parser, maxLength: 17 } + return { + parser, + maxLength: 17, + } } export function cramBlockCrc32() { diff --git a/src/cramFile/slice/index.ts b/src/cramFile/slice/index.ts index 9b53b9e..931a67c 100644 --- a/src/cramFile/slice/index.ts +++ b/src/cramFile/slice/index.ts @@ -192,9 +192,6 @@ export default class CramSlice { const { majorVersion } = await this.file.getDefinition() const sectionParsers = getSectionParsers(majorVersion) const containerHeader = await this.container.getHeader() - if (!containerHeader) { - throw new Error('no container header detected') - } const header = await this.file.readBlock( containerHeader._endPosition + this.containerPosition, diff --git a/test/__snapshots__/dump1.test.ts.snap b/test/__snapshots__/dump1.test.ts.snap index c5cbea6..2065c70 100644 --- a/test/__snapshots__/dump1.test.ts.snap +++ b/test/__snapshots__/dump1.test.ts.snap @@ -2388374,554 +2388374,6 @@ exports[`can dump the whole human_g1k_v37.20.21.1-100#NA12878.20.21.1-100.100-Se }, ], }, - { - "compressionScheme": { - "APdelta": true, - "dataSeriesEncoding": { - "AP": { - "codecId": 3, - "parameters": { - "bitLengths": [ - 0, - ], - "numCodes": 1, - "numLengths": 1, - "symbols": [ - 0, - ], - }, - "parametersBytes": 4, - }, - "BA": { - "codecId": 3, - "parameters": { - "bitLengths": [ - 2, - 2, - 2, - 2, - ], - "numCodes": 4, - "numLengths": 4, - "symbols": [ - 65, - 67, - 71, - 84, - 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2, + "numRecords": 0, + "recordCounter": 0, + "refSeqId": 0, + "refSeqStart": 0, + }, + { + "samHeader": [], + }, + { + "samHeader": [], + }, + ], + }, +] +`; + +exports[`can dump the whole ce#unmap1.2.1.cram without error 1`] = ` +[ + { + "fileId": "-", + "magic": "CRAM", + "majorVersion": 2, + "minorVersion": 1, + }, + { + "containerHeader": { + "_endPosition": 39, + "_size": 13, + "alignmentSpan": 0, + "landmarks": [ + 0, + ], + "length": 10819, + "numBases": 0, + "numBlocks": 1, + "numLandmarks": 1, + "numRecords": 0, + "recordCounter": 0, + "refSeqId": 0, + "refSeqStart": 0, + }, + "data": [ + { + "_endPosition": 39, + "_size": 13, + "alignmentSpan": 0, + "landmarks": [ + 0, + ], + "length": 10819, + "numBases": 0, + "numBlocks": 1, + "numLandmarks": 1, + "numRecords": 0, + "recordCounter": 0, + "refSeqId": 0, + "refSeqStart": 0, + }, + { + "samHeader": [ + { + "data": [ + { + "tag": "VN", + "value": "1.0", + }, + { + "tag": "SO", + "value": "unsorted", + }, + ], + "tag": "HD", + 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- 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - 2, - ], - "readBases": "NTACTTCTTACAAGATTTTTATCGCTACTTGAAAAAAATTCATCAACATAATCGCCATGACTATCTGCACCGTGAGTATGATAAGCAGCAACTCTATCTG", - "readGroupId": -1, - "readLength": 100, - "readName": "SRR065390.33808523", - "sequenceId": -1, - "tags": { - "YT": "UU", - }, - "templateSize": 0, - "uniqueId": 835, - }, - ], - "header": { - "_endPosition": 865, - "_size": 40, - "compressedSize": 36, - "compressionMethod": "raw", - "content": { - "data": [ - 255, - 255, - 255, - 255, - 15, - 0, - 1, - 10, - 0, - 5, - 4, - 9, - 11, - 12, - 30, - 255, - 255, - 255, - 255, + 5, + 4, + 11, + 12, + 30, + 224, + 89, + 84, + 90, + 255, + 255, + 255, + 255, 15, 0, 0, @@ -2967274,17 +2972628,17 @@ exports[`can dump the whole ce#unmap1.3.0.cram without error 1`] = ` "type": "Buffer", }, "contentId": 0, - "contentPosition": 825, + "contentPosition": 3387, "contentType": "MAPPED_SLICE_HEADER", - "crc32": 210895449, + "crc32": 4132320682, "parsedContent": { - "_endPosition": 664, - "_size": 36, + "_endPosition": 2722, + "_size": 39, "contentIds": [ - 9, 11, 12, 30, + 5854298, ], "md5": [ 0, @@ -2967306,14 +2972660,14 @@ exports[`can dump the whole ce#unmap1.3.0.cram without error 1`] = ` ], "numBlocks": 5, "numContentIds": 4, - "numRecords": 10, - "recordCounter": 0, + "numRecords": 2, + "recordCounter": 17, "refBaseBlockId": -1, - "refSeqId": -1, - "refSeqSpan": 1, + "refSeqId": -2, + "refSeqSpan": 0, "refSeqStart": 0, }, - "uncompressedSize": 36, + "uncompressedSize": 39, }, }, ], @@ -2967321,28 +2972675,26 @@ exports[`can dump the whole ce#unmap1.3.0.cram without error 1`] = ` ] `; -exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` +exports[`can dump the whole cram_query_sorted.cram without error 1`] = ` [ { "fileId": "-", "magic": "CRAM", - "majorVersion": 3, - "minorVersion": 0, + "majorVersion": 2, + "minorVersion": 1, }, { "containerHeader": { - "_endPosition": 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-2967386,15 +2972736,15 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "ID", - "value": "bowtie2", + "value": "1", }, { "tag": "PN", - "value": "bowtie2", + "value": "Hey!", }, { "tag": "VN", - "value": "2.0.0-beta5", + "value": "2.0", }, ], "tag": "PG", @@ -2967403,213 +2972753,40 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_I", - }, - { - "tag": "LN", - "value": "1009800", - }, - { - "tag": "M5", - "value": "8ede36131e0dbf3417807e48f77f3ebd", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_II", - }, - { - "tag": "LN", - "value": "5000", - }, - { - "tag": "M5", - "value": "8e7993f7a93158587ee897d7287948ec", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_III", - }, - { - "tag": "LN", - "value": "5000", - }, - { - "tag": "M5", - "value": "3adcb065e1cf74fafdbba1e8c352b323", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_IV", - }, - { - "tag": "LN", - "value": "5000", - }, - { - "tag": "M5", - "value": "251af66a69ee589c9f3757340ec2de6f", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_V", - }, - { - "tag": "LN", - "value": "5000", - }, - { - "tag": "M5", - "value": "cf200a65fb754836dcc56b24b3170ee8", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_X", - }, - { - "tag": "LN", - "value": "5000", - }, - { - "tag": "M5", - "value": "6f9368fd2192c89c613718399d2d31fc", - }, - { - "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", - }, - ], - "tag": "SQ", - }, - { - "data": [ - { - "tag": "SN", - "value": "CHROMOSOME_MtDNA", + "value": "chr1", }, { "tag": "LN", - "value": "5000", + "value": "101", }, { "tag": "M5", - "value": "cd05857ece6411f40257a565ccfe15bb", + "value": "bd01f7e11515bb6beda8f7257902aa67", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", }, - { - "data": [ - { - "tag": "ID", - "value": "UNKNOWN", - }, - { - "tag": "SM", - "value": "UNKNOWN", - }, - ], - "tag": "RG", - }, - ], - }, - { - "samHeader": [ - { - "data": [ - { - "tag": "VN", - "value": "1.0", - }, - { - "tag": "SO", - "value": "unsorted", - }, - ], - "tag": "HD", - }, - { - "data": [ - { - "tag": "ID", - "value": "bowtie2", - }, - { - "tag": "PN", - "value": "bowtie2", - }, - { - "tag": "VN", - "value": "2.0.0-beta5", - }, - ], - "tag": "PG", - }, { "data": [ { "tag": "SN", - "value": "CHROMOSOME_I", + "value": "chr2", }, { "tag": "LN", - "value": "1009800", + "value": "101", }, { "tag": "M5", - "value": "8ede36131e0dbf3417807e48f77f3ebd", + "value": "31c33e2155b3de5e2554b693c475b310", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967618,19 +2972795,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_II", + "value": "chr3", }, { "tag": "LN", - "value": "5000", + "value": "101", }, { "tag": "M5", - "value": "8e7993f7a93158587ee897d7287948ec", + "value": "631593c6dd2048ae88dcce2bd505d295", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967639,19 +2972816,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_III", + "value": "chr4", }, { "tag": "LN", - "value": "5000", + "value": "101", }, { "tag": "M5", - "value": "3adcb065e1cf74fafdbba1e8c352b323", + "value": "c60cb92f1ee5b78053c92bdbfa19abf1", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967660,19 +2972837,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_IV", + "value": "chr5", }, { "tag": "LN", - "value": "5000", + "value": "101", }, { "tag": "M5", - "value": "251af66a69ee589c9f3757340ec2de6f", + "value": "07ebc213c7611db0eacbb1590c3e9bda", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967681,19 +2972858,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_V", + "value": "chr6", }, { "tag": "LN", - "value": "5000", + "value": "101", }, { "tag": "M5", - "value": "cf200a65fb754836dcc56b24b3170ee8", + "value": "7be2f5e7ee39e60a6c3b5b6a41178c6d", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967702,19 +2972879,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_X", + "value": "chr7", }, { "tag": "LN", - "value": "5000", + "value": "404", }, { "tag": "M5", - "value": "6f9368fd2192c89c613718399d2d31fc", + "value": "da488fc432cdaf2c20c96da473a7b630", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967723,19 +2972900,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "SN", - "value": "CHROMOSOME_MtDNA", + "value": "chr8", }, { "tag": "LN", - "value": "5000", + "value": "202", }, { "tag": "M5", - "value": "cd05857ece6411f40257a565ccfe15bb", + "value": "d339678efce576d5546e88b49a487b63", }, { "tag": "UR", - "value": "/Users/rbuels/dev/htslib/test/ce.fa", + "value": "/home/chris/projects/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/count_reads.fasta", }, ], "tag": "SQ", @@ -2967744,11 +2972921,11 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "data": [ { "tag": "ID", - "value": "UNKNOWN", + "value": "0", }, { "tag": "SM", - "value": "UNKNOWN", + "value": "Hi,Mom!", }, ], "tag": "RG", @@ -2967759,50 +2972936,46 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` }, { "compressionScheme": { - "APdelta": true, + "APdelta": false, "dataSeriesEncoding": { "AP": { + "codecId": 6, + "parameters": { + "length": 9, + "offset": 0, + }, + "parametersBytes": 2, + }, + "BF": { "codecId": 3, "parameters": { "bitLengths": [ - 0, + 2, + 2, + 2, + 3, + 3, ], - "numCodes": 1, - "numLengths": 1, + "numCodes": 5, + "numLengths": 5, "symbols": [ - 0, + 99, + 147, + 163, + 83, + 89, ], }, - "parametersBytes": 4, + "parametersBytes": 14, }, - "BA": { + "BS": { "codecId": 1, "parameters": { - "blockContentId": 30, + "blockContentId": 31, }, "parametersBytes": 1, }, - "BB": { - "codecId": 4, - "parameters": { - "lengthsEncoding": { - "codecId": 1, - "parameters": { - "blockContentId": 42, - }, - "parametersBytes": 1, - }, - "valuesEncoding": { - "codecId": 1, - "parameters": { - "blockContentId": 37, - }, - "parametersBytes": 1, - }, - }, - "parametersBytes": 6, - }, - "BF": { + "CF": { "codecId": 3, "parameters": { "bitLengths": [ @@ -2967811,12 +2972984,12 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - 4, + 3, ], }, "parametersBytes": 4, }, - "CF": { + "FC": { "codecId": 3, "parameters": { "bitLengths": [ @@ -2967825,11 +2972998,38 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - 3, + 88, ], }, "parametersBytes": 4, }, + "FN": { + "codecId": 3, + "parameters": { + "bitLengths": [ + 2, + 2, + 2, + 2, + ], + "numCodes": 4, + "numLengths": 4, + "symbols": [ + 21, + 75, + 82, + 88, + ], + }, + "parametersBytes": 10, + }, + "FP": { + "codecId": 1, + "parameters": { + "blockContentId": 28, + }, + "parametersBytes": 1, + }, "IN": { "codecId": 5, "parameters": { @@ -2967842,15 +2973042,19 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "codecId": 3, "parameters": { "bitLengths": [ - 0, + 1, + 2, + 2, ], - "numCodes": 1, - "numLengths": 1, + "numCodes": 3, + "numLengths": 3, "symbols": [ + 1, 0, + 2, ], }, - "parametersBytes": 4, + "parametersBytes": 8, }, "MQ": { "codecId": 3, @@ -2967861,38 +2973065,48 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - 0, + 255, ], }, - "parametersBytes": 4, + "parametersBytes": 5, }, "NP": { "codecId": 3, "parameters": { "bitLengths": [ - 0, + 2, + 2, + 2, + 3, + 3, ], - "numCodes": 1, - "numLengths": 1, + "numCodes": 5, + "numLengths": 5, "symbols": [ + 16, + 21, + 302, 0, + 1, ], }, - "parametersBytes": 4, + "parametersBytes": 13, }, "NS": { "codecId": 3, "parameters": { "bitLengths": [ - 0, + 1, + 1, ], - "numCodes": 1, - "numLengths": 1, + "numCodes": 2, + "numLengths": 2, "symbols": [ -1, + 6, ], }, - "parametersBytes": 8, + "parametersBytes": 10, }, "QS": { "codecId": 1, @@ -2967910,10 +2973124,10 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - -1, + 0, ], }, - "parametersBytes": 8, + "parametersBytes": 4, }, "RI": { "codecId": 3, @@ -2967924,10 +2973138,10 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - -1, + 6, ], }, - "parametersBytes": 8, + "parametersBytes": 4, }, "RL": { "codecId": 3, @@ -2967938,7 +2973152,7 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "numCodes": 1, "numLengths": 1, "symbols": [ - 100, + 101, ], }, "parametersBytes": 4, @@ -2967977,15 +2973191,23 @@ exports[`can dump the whole ce#unmap1.tmp.cram without error 1`] = ` "codecId": 3, "parameters": { "bitLengths": [ - 0, + 2, + 2, + 2, + 3, + 3, ], - "numCodes": 1, - "numLengths": 1, + "numCodes": 5, + "numLengths": 5, "symbols": [ + -201, + -96, + 201, 0, + 96, ], }, - "parametersBytes": 4, + "parametersBytes": 21, }, }, "readNamesIncluded": true, @@ 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a/test/__snapshots__/parse.test.ts.snap +++ b/test/__snapshots__/parse.test.ts.snap @@ -38,9 +38,9 @@ exports[`CRAM reader > can count containers in ce#tag_depadded.tmp.cram 1`] = `2 exports[`CRAM reader > can count containers in ce#tag_padded.tmp.cram 1`] = `2`; -exports[`CRAM reader > can count containers in ce#unmap.tmp.cram 1`] = `2`; +exports[`CRAM reader > can count containers in ce#unmap.tmp.cram 1`] = `1`; -exports[`CRAM reader > can count containers in ce#unmap1.tmp.cram 1`] = `2`; +exports[`CRAM reader > can count containers in ce#unmap1.tmp.cram 1`] = `1`; exports[`CRAM reader > can count containers in ce#unmap2.tmp.cram 1`] = `3`; diff --git a/test/parse.test.ts b/test/parse.test.ts index d1110ce..1b3ff8e 100644 --- a/test/parse.test.ts +++ b/test/parse.test.ts @@ -62,49 +62,48 @@ describe('CRAM reader', () => { refSeqStart: 1, }) }) - - Object.entries({ - 'auxf#values.tmp.cram': 2, - 'c1#bounds.tmp.cram': 2, - 'c1#clip.tmp.cram': 2, - 'c1#noseq.tmp.cram': 2, - 'c1#pad1.tmp.cram': 2, - 'c1#clip.2.1.cram': 2, - 'c1#pad2.tmp.cram': 2, - 'c1#pad3.tmp.cram': 2, - 'c1#unknown.tmp.cram': 2, - 'c2#pad.tmp.cram': 2, - 'ce#1.tmp.cram': 2, - 'ce#1000.tmp.cram': 30, - 'ce#2.tmp.cram': 2, - 'ce#5.tmp.cram': 2, - 'ce#5b.tmp.cram': 4, - 'ce#large_seq.tmp.cram': 2, - 'ce#supp.tmp.cram': 2, - 'ce#tag_depadded.tmp.cram': 2, - 'ce#tag_padded.tmp.cram': 2, - 'ce#unmap.tmp.cram': 2, - 'ce#unmap1.tmp.cram': 2, - 'ce#unmap2.tmp.cram': 3, - 'headernul.tmp.cram': 2, - 'md#1.tmp.cram': 2, - 'sam_alignment.tmp.cram': 2, - 'xx#blank.tmp.cram': 1, - 'xx#large_aux.tmp.cram': 2, - 'xx#large_aux2.tmp.cram': 2, - 'xx#minimal.tmp.cram': 3, - 'xx#pair.tmp.cram': 2, - 'xx#repeated.tmp.cram': 2, - 'xx#rg.tmp.cram': 2, - 'xx#tlen.tmp.cram': 3, - 'xx#tlen2.tmp.cram': 3, - 'xx#triplet.tmp.cram': 3, - 'xx#unsorted.tmp.cram': 4, - }).forEach(([filename, containerCount]) => { - it(`can count ${containerCount} containers in ${filename}`, async () => { + ;[ + 'auxf#values.tmp.cram', + 'c1#bounds.tmp.cram', + 'c1#clip.tmp.cram', + 'c1#noseq.tmp.cram', + 'c1#pad1.tmp.cram', + 'c1#clip.2.1.cram', + 'c1#pad2.tmp.cram', + 'c1#pad3.tmp.cram', + 'c1#unknown.tmp.cram', + 'c2#pad.tmp.cram', + 'ce#1.tmp.cram', + 'ce#1000.tmp.cram', + 'ce#2.tmp.cram', + 'ce#5.tmp.cram', + 'ce#5b.tmp.cram', + 'ce#large_seq.tmp.cram', + 'ce#supp.tmp.cram', + 'ce#tag_depadded.tmp.cram', + 'ce#tag_padded.tmp.cram', + 'ce#unmap.tmp.cram', + 'ce#unmap1.tmp.cram', + 'ce#unmap2.tmp.cram', + 'headernul.tmp.cram', + 'md#1.tmp.cram', + 'sam_alignment.tmp.cram', + 'xx#blank.tmp.cram', + 'xx#large_aux.tmp.cram', + 'xx#large_aux2.tmp.cram', + 'xx#minimal.tmp.cram', + 'xx#pair.tmp.cram', + 'xx#repeated.tmp.cram', + 'xx#rg.tmp.cram', + 'xx#tlen.tmp.cram', + 'xx#tlen2.tmp.cram', + 'xx#triplet.tmp.cram', + 'xx#unsorted.tmp.cram', + ].forEach(filename => { + it(`can count containers in ${filename}`, async () => { const file = new CramFile({ filehandle: testDataFile(filename) }) const count = await file.containerCount() - expect(count).toEqual(containerCount) + expect(count).toMatchSnapshot() }) })