diff --git a/test/__snapshots__/dump2.test.ts.snap b/test/__snapshots__/dump2.test.ts.snap index eb258c74..5feef36a 100644 --- a/test/__snapshots__/dump2.test.ts.snap +++ b/test/__snapshots__/dump2.test.ts.snap @@ -1,5 +1,24237 @@ // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html +exports[`can dump the whole ML_test.cram without error 1`] = ` +[ + { + "fileId": "-", + "magic": "CRAM", + "majorVersion": 3, + "minorVersion": 0, + }, + { + "containerHeader": { + "_endPosition": 45, + "_size": 19, + "alignmentSpan": 0, + "crc32": 2194198519, + "landmarks": [ + 0, + 5940, + ], + "length": 8921, + "numBases": 0, + "numBlocks": 2, + "numLandmarks": 2, + "numRecords": 0, + "recordCounter": 0, + "refSeqId": 0, + "refSeqStart": 0, + }, + "data": [ + { + "_endPosition": 45, + "_size": 19, + "alignmentSpan": 0, + "crc32": 2194198519, + "landmarks": [ + 0, + 5940, + ], + "length": 8921, + "numBases": 0, + "numBlocks": 2, + "numLandmarks": 2, + "numRecords": 0, + "recordCounter": 0, + 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"C+h?,26,0,8,0,0,16,2,0,9,0,6,12,4,1,2,4,3,0,3,1,4,3,1,3,2,5,16,20,4,1,13,2,5,3,3,4,10,3,6,3,10,0,14,16,14,3,10,3,8,3,8,2,10,2,10,2,10,2,9,10,9,2,3,18,15,2,11,3,0,9,9,5,17,7,7,9,2,2,5,0,14,9,5,1,3,6,4,12,9,0,6,2,7,1,0,6,1,8,0,6,2,9,9,8,5,1,2,2,1,1,4,17,18,4,4,3,2,0,1,3,7,3,0,0,1,2,3,9,3,10,21,3,2,7,48,7,13,1,1,5,10,10,4,1,7,12,5,5,0,7,17,15,72,32,0,1,2,1,2,5,7,3,23,0,0,9,16,10,19,1,4,19,14,1,4,4,11,33,1,7,5,7,9,24,1,8,4,16,3,19,2,29,20,10,17,4,15,7,11,0,21,14,1,5,0,22,18,17,1,7,4,3,47,32,5,3,10,19,2,35,39,28,2,0,2,8,19,0,8,7,0,4,17,142,14,11,6,3,24,25,4,14,34,1,39,2,18,23,21,7,12,6,1,68,28,6,9,21,39,7,20,42,5,15,2,12,4,2,4,4,2,3,4,1,1,2,2,7,3,0,17,11,3,13,3,11,1,12,0,15,2,6,13,8,10,2,6,15,3,2,1,24,20,31,25,27,6,2,7,6,57,8,7,23,7,2,4,1,5,12,2,3,0,2,9,76,8,11;C+m?,26,0,8,0,0,16,2,0,9,0,6,12,4,1,2,4,3,0,3,1,4,3,1,3,2,5,16,20,4,1,13,2,5,3,3,4,10,3,6,3,10,0,14,16,14,3,10,3,8,3,8,2,10,2,10,2,10,2,9,10,9,2,3,18,15,2,11,3,0,9,9,5,17,7,7,9,2,2,5,0,14,9,5,1,3,6,4,12,9,0,6,2,7,1,0,6,1,8,0,6,2,9,9,8,5,1,2,2,1,1,4,17,18,4,4,3,2,0,1,3,7,3,0,0,1,2,3,9,3,10,21,3,2,7,48,7,13,1,1,5,10,10,4,1,7,12,5,5,0,7,17,15,72,32,0,1,2,1,2,5,7,3,23,0,0,9,16,10,19,1,4,19,14,1,4,4,11,33,1,7,5,7,9,24,1,8,4,16,3,19,2,29,20,10,17,4,15,7,11,0,21,14,1,5,0,22,18,17,1,7,4,3,47,32,5,3,10,19,2,35,39,28,2,0,2,8,19,0,8,7,0,4,17,142,14,11,6,3,24,25,4,14,34,1,39,2,18,23,21,7,12,6,1,68,28,6,9,21,39,7,20,42,5,15,2,12,4,2,4,4,2,3,4,1,1,2,2,7,3,0,17,11,3,13,3,11,1,12,0,15,2,6,13,8,10,2,6,15,3,2,1,24,20,31,25,27,6,2,7,6,57,8,7,23,7,2,4,1,5,12,2,3,0,2,9,76,8,11;", + "cm": 1988, + "de": 0.011699999682605267, + "ms": 25593, + "nn": 0, + "rl": 1521, + "s1": 11574, + "s2": 57, + "tp": "P", + }, + "templateSize": 0, + "uniqueId": 9423, + }, + ], + "header": { + "_endPosition": 9511, + "_size": 89, + "compressedSize": 85, + "compressionMethod": "raw", + "content": { + "data": [ + 15, + 225, + 104, + 163, + 74, + 180, + 36, + 1, + 0, + 21, + 20, + 11, + 12, + 13, + 14, + 27, + 28, + 29, + 30, + 31, + 224, + 116, + 112, + 65, + 224, + 115, + 50, + 67, + 224, + 115, + 49, + 83, + 224, + 65, + 83, + 83, + 224, + 77, + 76, + 66, + 224, + 109, + 115, + 83, + 224, + 100, + 101, + 102, + 224, + 114, + 108, + 83, + 224, + 110, + 110, + 67, + 224, + 77, + 77, + 90, + 224, + 99, + 109, + 83, + 255, + 255, + 255, + 255, + 15, + 21, + 63, + 221, + 6, + 39, + 142, + 26, + 80, + 141, + 166, + 163, + 58, + 127, + 68, + 76, + 48, + ], + "type": "Buffer", + }, + "contentId": 0, + "contentPosition": 9422, + "contentType": "MAPPED_SLICE_HEADER", + "crc32": 2748715591, + "parsedContent": { + "_endPosition": 9074, + "_size": 85, + "contentIds": [ + 11, + 12, + 13, + 14, + 27, + 28, + 29, + 30, + 31, + 7630913, + 7549507, + 7549267, + 4281171, + 5065794, + 7172947, + 6579558, + 7498835, + 7237187, + 5066074, + 6516051, + ], + "md5": [ + 21, + 63, + 221, + 6, + 39, + 142, + 26, + 80, + 141, + 166, + 163, + 58, + 127, + 68, + 76, + 48, + ], + "numBlocks": 21, + "numContentIds": 20, + "numRecords": 1, + "recordCounter": 0, + "refBaseBlockId": -1, + "refSeqId": 15, + "refSeqSpan": 13348, + "refSeqStart": 23634762, + }, + "uncompressedSize": 85, + }, + }, + ], + }, +] +`; + exports[`can dump the whole auxf#test2.cram without error 1`] = ` [ { diff --git a/test/data/ML_test.cram b/test/data/ML_test.cram new file mode 100644 index 00000000..057bc3ab Binary files /dev/null and b/test/data/ML_test.cram differ diff --git a/test/lib/testFileList.ts b/test/lib/testFileList.ts index 2b61eb14..6f77be31 100644 --- a/test/lib/testFileList.ts +++ b/test/lib/testFileList.ts @@ -118,6 +118,7 @@ xx#unsorted.2.1.cram xx#unsorted.3.0.cram xx#unsorted.tmp.cram grc37-1#HG03297.mapped.ILLUMINA.bwa.ESN.low_coverage.20130415.bam.cram +ML_test.cram ` .split(/\s+/) .filter(f => !!f)