{ "format": "oscr-script-manifest/1", "repository": "github.com/alexdobin/star", "url": "https://github.com/alexdobin/STAR", "host": "github.com", "commit": "b1edc1208d91a53bf40ebae8669f71d50b994851", "license": "MIT", "license_confirmed_by": "license file LICENSE", "redistribution": "yes", "files": [ { "path": "LICENSE", "sha256": "551e5bc4f91bf85b75c848aabba5acbcff4f4adf75e606cd17787038a155e69f", "language": "License", "lines": 21, "truncated": false, "block": 3, "row": 8023 }, { "path": "README.md", "sha256": "702eb50c9aa3e0ab3a8bcd251eca90ab8dd4cf3833d9bcdf25db218ce669e3e3", "language": "Text", "lines": 115, "truncated": false, "block": 4, "row": 2486 }, { "path": "extras/scripts/extractSJfromGTF.sh", "sha256": "356b312af0e585f87f6596f3771f70e3fdd707024d96feeccaffc72d08522086", "language": "Shell", "lines": 10, "truncated": false, "block": 4, "row": 1393 }, { "path": "extras/scripts/sjMotif.m", "sha256": "4e1ea6d0c0c148099ad2b49b1d2d9e4e7564a94684e92873e9394294f7dd4ce1", "language": "MATLAB", "lines": 45, "truncated": false, "block": 3, "row": 10158 }, { "path": "source/AlignVsTranscript.h", "sha256": "c3713f7dfff0f2e66c38170cdae17cdc8bad257f55b507f9d113dc1e22ba8148", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3334 }, { "path": "source/BAMbinSortByCoordinate.cpp", "sha256": "c6db83dea84586227b9c33455f044a14bc4c071598bcfdb13f9d14ce55d257ff", "language": "C++", "lines": 81, "truncated": false, "block": 3, "row": 2255 }, { "path": "source/BAMbinSortByCoordinate.h", "sha256": "f42323a77e39386c9e93da9818c274e2a8947c318aba19f39f677169a4fedc68", "language": "C/C++", "lines": 12, "truncated": false, "block": 3, "row": 3382 }, { "path": "source/BAMbinSortUnmapped.cpp", "sha256": "ed4bf4e1866f89fb69f3293346da6e6a5eca685f48d7abbfeb091fdcf6476853", "language": "C++", "lines": 91, "truncated": false, "block": 3, "row": 2345 }, { "path": "source/BAMbinSortUnmapped.h", "sha256": "e8be7aa723afb4fc7db0e2eab13b6e50732571457d510092d4b100069cdb5020", "language": "C/C++", "lines": 12, "truncated": false, "block": 3, "row": 3370 }, { "path": "source/BAMfunctions.cpp", "sha256": "ca7faa893c749db90777b2e5c48ddb56bb91c5159483ba22c0cd36b5e295df92", "language": "C++", "lines": 194, "truncated": false, "block": 3, "row": 2767 }, { "path": "source/BAMfunctions.h", "sha256": "24ae61be831accbec19b46a87e227821b8d704707d0df448025fce0de1e8ca88", "language": "C/C++", "lines": 79, "truncated": false, "block": 3, "row": 3946 }, { "path": "source/BAMoutput.cpp", "sha256": "12b8e120b181964996f47177195bbe52a25cfdc605fa9614930a6a5cc9e00fcc", "language": "C++", "lines": 186, "truncated": false, "block": 3, "row": 2791 }, { "path": "source/BAMoutput.h", "sha256": "0fc676c33b0748fcd216a1cf4152946d050e53497777b8c2f6de1c06778572e5", "language": "C/C++", "lines": 37, "truncated": false, "block": 3, "row": 3571 }, { "path": "source/Chain.cpp", "sha256": "d48d64e7ba78d6d13382e0fdb93ab9641486251e77d56e3bf2cf5c67e8fc98ba", "language": "C++", "lines": 126, "truncated": false, "block": 3, "row": 2520 }, { "path": "source/Chain.h", "sha256": "d7a2922315abc3ccf4cb5a4fc3ba3366238aad40838da04ce8dec3e9a5f86471", "language": "C/C++", "lines": 30, "truncated": false, "block": 3, "row": 3440 }, { "path": "source/ChimericAlign.cpp", "sha256": "349be7139d8518b3864a6680e9d01662283dcc6b4d296903c49eb5d504c7650e", "language": "C++", "lines": 32, "truncated": false, "block": 3, "row": 1492 }, { "path": "source/ChimericAlign.h", "sha256": "b55c719978db9c56d22f4183f61b9c581ae3fe51f9a7c84744e714871923be9c", "language": "C/C++", "lines": 41, "truncated": false, "block": 3, "row": 3595 }, { "path": "source/ChimericAlign_chimericBAMoutput.cpp", "sha256": "076d74764691a18af95b53b9388a677be9b2b3acfb3ad9edfb06d2ffcf894f9a", "language": "C++", "lines": 105, "truncated": false, "block": 3, "row": 2599 }, { "path": "source/ChimericAlign_chimericJunctionOutput.cpp", "sha256": "8fe67cefcd859e657f9d1f2881dfe5757cb7aa2c16f871fde19bbc8f581b6649", "language": "C++", "lines": 23, "truncated": false, "block": 3, "row": 1686 }, { "path": "source/ChimericAlign_chimericStitching.cpp", "sha256": "7e004ab84473afa1d914fce54c4ee7b1a92e7ae6d5058f840d7c19af29978cd4", "language": "C++", "lines": 181, "truncated": false, "block": 3, "row": 2742 }, { "path": "source/ChimericDetection.cpp", "sha256": "c9182a6284abc57f1b3755af8f4daf55479ca192810442f9c857bffcf797b5bd", "language": "C++", "lines": 6, "truncated": false, "block": 3, "row": 702 }, { "path": "source/ChimericDetection.h", "sha256": "e25c2390ebd9b48102e51d4cf0f73062cdcd606b7c224e9986610524a0ba4352", "language": "C/C++", "lines": 29, "truncated": false, "block": 3, "row": 3449 }, { "path": "source/ChimericDetection_chimericDetectionMult.cpp", "sha256": "6c7d9250fbb1b72b38c67ce16d3b4ea1f3f47ced34a8388e30f3daa601729985", "language": "C++", "lines": 138, "truncated": false, "block": 3, "row": 2728 }, { "path": "source/ChimericSegment.cpp", "sha256": "04626d428b777f80ef6e38a1c4ec1ceaa85039f2916911f7c8b00c3a808cad74", "language": "C++", "lines": 32, "truncated": false, "block": 3, "row": 1672 }, { "path": "source/ChimericSegment.h", "sha256": "bb086a8ab9621e859469bcf4b04f68ee8ca408e5949cda8f8e2fc7722fc2f6a1", "language": "C/C++", "lines": 23, "truncated": false, "block": 3, "row": 3420 }, { "path": "source/ChimericTranscript.h", "sha256": "d010357e10b6c898d626af8ea95d3517d623390a3b996176405215c41f8ad0d6", "language": "C/C++", "lines": 19, "truncated": false, "block": 3, "row": 3412 }, { "path": "source/ClipCR4.cpp", "sha256": "ff398e5cce959ee753e913c9497376151598ea2b788721d722bbab9552cf64a3", "language": "C++", "lines": 109, "truncated": false, "block": 3, "row": 2070 }, { "path": "source/ClipCR4.h", "sha256": "ac05d9bd4b89046b83732e1ccc1706882f7e0a6a2b34b9857e2cbd42b51446ec", "language": "C/C++", "lines": 41, "truncated": false, "block": 3, "row": 3458 }, { "path": "source/ClipMate.h", "sha256": "0c9b461e6b4e28931f3f871bc70bec540a68bc3aaa98181673d7a47cfa2dc95b", "language": "C/C++", "lines": 34, "truncated": false, "block": 3, "row": 3456 }, { "path": "source/ClipMate_clip.cpp", "sha256": "5984fcab7743aebb2e1c3a79c650d61ab7477a6b824ef1b6d8132338f92912ae", "language": "C++", "lines": 78, "truncated": false, "block": 3, "row": 1919 }, { "path": "source/ClipMate_clipChunk.cpp", "sha256": "f685a456665f8f3f6e6b56b149d11d76c00de9157352b7f60da8b8f3542046b4", "language": "C++", "lines": 62, "truncated": false, "block": 3, "row": 1742 }, { "path": "source/ClipMate_initialize.cpp", "sha256": "55488425a7f78fd92ea5b366be8f9c0b4c5c533bc68b97163fca8ce7036a7e5e", "language": "C++", "lines": 32, "truncated": false, "block": 3, "row": 1011 }, { "path": "source/ErrorWarning.cpp", "sha256": "e0931d14f98a1916abb99ec344fb50ffd68bd5a63a49855586a1b41f1d753a18", "language": "C++", "lines": 37, "truncated": false, "block": 3, "row": 1402 }, { "path": "source/ErrorWarning.h", "sha256": "f2e927b958a4230c6fd85535203e2e711ff4d651c8060add98d58f85a8639671", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3377 }, { "path": "source/GTF.cpp", "sha256": "9254afb2a2fa8ff3e751d9bfafd2b86f4d389ee8b6e647ad09416dd61962229c", "language": "C++", "lines": 171, "truncated": false, "block": 3, "row": 2888 }, { "path": "source/GTF.h", "sha256": "4fb9ffd8118f9a97762d392cd5dd950dbdad6cd9888f06119febb4116a98224f", "language": "C/C++", "lines": 36, "truncated": false, "block": 3, "row": 3475 }, { "path": "source/GTF_superTranscript.cpp", "sha256": "6553a3ebeda538df7327b91730c7d63b3477aecdd77d4e0f95c9d1b87a673f29", "language": "C++", "lines": 257, "truncated": false, "block": 3, "row": 3064 }, { "path": "source/GTF_transcriptGeneSJ.cpp", "sha256": "dccd988d45418def20a8086fadb7b57a15b9a703e1ccc3586dc3642286c2c297", "language": "C++", "lines": 183, "truncated": false, "block": 3, "row": 2918 }, { "path": "source/Genome.cpp", "sha256": "ee10043fa3c0053ad4e587fa5ffe2c6baf51e552613ce0a60182c84f1dac0126", "language": "C++", "lines": 234, "truncated": false, "block": 3, "row": 2990 }, { "path": "source/Genome.h", "sha256": "9483ed26c8739a4c04cc85856257bb0142a6c66a95666e1b3e5333f3b5ee5112", "language": "C/C++", "lines": 107, "truncated": false, "block": 3, "row": 4023 }, { "path": "source/Genome_genomeGenerate.cpp", "sha256": "3d8fe6cf3685e25cc76c3dcfba12ed68ff2b5946bab22ddedc7996a077ba2124", "language": "C++", "lines": 438, "truncated": false, "block": 3, "row": 3176 }, { "path": "source/Genome_genomeLoad.cpp", "sha256": "f6a85ef14d13e814d3291ee86ce17599590fb778f65268bbe2eafdf37bc77542", "language": "C++", "lines": 521, "truncated": false, "block": 3, "row": 3214 }, { "path": "source/Genome_genomeOutLoad.cpp", "sha256": "51d51a2a4f665b6ee6d9158cc9cc07fc21ef2ed075c67e87912909eedf6410d9", "language": "C++", "lines": 58, "truncated": false, "block": 3, "row": 1851 }, { "path": "source/Genome_insertSequences.cpp", "sha256": "8a72b76d09291d81ca49fcc395ff193803bc4d6144c107e35e5a6a175ea08c7a", "language": "C++", "lines": 33, "truncated": false, "block": 3, "row": 1386 }, { "path": "source/Genome_transformGenome.cpp", "sha256": "3b0807d1543e0a10cda68cfff9d19849e157048d4976191cd1e44b7efa96c12e", "language": "C++", "lines": 324, "truncated": false, "block": 3, "row": 3087 }, { "path": "source/GlobalVariables.cpp", "sha256": "f4ccc14a0adadc10b2a124adde5244813c611bcc88210d2ed544c08e06fd6020", "language": "C++", "lines": 4, "truncated": false, "block": 3, "row": 452 }, { "path": "source/GlobalVariables.h", "sha256": "15f402cde661a5cc115382d805f4c07e41640dfea1e54b8f692c97acae8e9ae9", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3328 }, { "path": "source/InOutStreams.cpp", "sha256": "14d75d256e0ce9e350bdeff6d9d7162cd44626f7e3cbd116a060c270a149b453", "language": "C++", "lines": 44, "truncated": false, "block": 3, "row": 1187 }, { "path": "source/InOutStreams.h", "sha256": "a152688ffce13341f3ef96901a21537c065d2d79de0e20b588ae0d670687eede", "language": "C/C++", "lines": 23, "truncated": false, "block": 3, "row": 3419 }, { "path": "source/IncludeDefine.h", "sha256": "0a55688ea42ca47041f2e53011f311300be7891ac3b10bd9de7767bed62af956", "language": "C/C++", "lines": 255, "truncated": false, "block": 3, "row": 4133 }, { "path": "source/OutSJ.cpp", "sha256": "1e0383cf8ec87833993796388329b7697af2043eca5324034c60b3efd2f8c6ff", "language": "C++", "lines": 123, "truncated": false, "block": 3, "row": 2513 }, { "path": "source/OutSJ.h", "sha256": "c60630a0024845aef8cc778e18684e77195f90bc7ecc9c7918ce28c21b211099", "language": "C/C++", "lines": 59, "truncated": false, "block": 3, "row": 3695 }, { "path": "source/PackedArray.cpp", "sha256": "f1aeb9cfa77754d75bfd69b3a0816bd1318a4088c480a5934520f9f85aaf2586", "language": "C++", "lines": 43, "truncated": false, "block": 3, "row": 1239 }, { "path": "source/PackedArray.h", "sha256": "f876319310d0f3eb405dbd6dbc5c8e7793f360f07497dd46e52e80c7ce5ab77d", "language": "C/C++", "lines": 34, "truncated": false, "block": 3, "row": 3453 }, { "path": "source/ParameterInfo.h", "sha256": "be3bcaf9d18188bf3e29eda47dba2d644f2af43b343bdab5651e2d6d85f15670", "language": "C/C++", "lines": 112, "truncated": false, "block": 3, "row": 3943 }, { "path": "source/Parameters.cpp", "sha256": "f303bd6fb1d541924d9f501ffc5266b49f6bda48dfbf593b5ad0d139abd72ae1", "language": "C++", "lines": 1269, "truncated": false, "block": 3, "row": 3286 }, { "path": "source/Parameters.h", "sha256": "0bb9b86c1159f5fe1f12c241fc5ca3dc7d7a36f67f5bc26cc4fbd9dfbd723387", "language": "C/C++", "lines": 374, "truncated": false, "block": 3, "row": 4385 }, { "path": "source/ParametersChimeric.h", "sha256": "cd09b75ad62d3e892ecb314f746ec4c19b0706e9fd615f7d69bfc77f097a540b", "language": "C/C++", "lines": 41, "truncated": false, "block": 3, "row": 3485 }, { "path": "source/ParametersChimeric_initialize.cpp", "sha256": "12d46f39ff22e1a1cc9d5ee169946b1bf433827494b9aef8edfaf36451d07c60", "language": "C++", "lines": 118, "truncated": false, "block": 3, "row": 2579 }, { "path": "source/ParametersClip.h", "sha256": "4de79db0d8cda758a3cbbf7b8f9527297e55deb79d623565a0e5c521c5b21685", "language": "C/C++", "lines": 37, "truncated": false, "block": 3, "row": 3430 }, { "path": "source/ParametersClip_initialize.cpp", "sha256": "ca59ff54a49da94444d41d4595f6fd33bb6433ca1613803c5f021a345d90c8e1", "language": "C++", "lines": 107, "truncated": false, "block": 3, "row": 2609 }, { "path": "source/ParametersGenome.cpp", "sha256": "f7ae6d62627b976614c6e804846d9b3c7a89a442f8d73a5e591fee1a67194706", "language": "C++", "lines": 59, "truncated": false, "block": 3, "row": 2052 }, { "path": "source/ParametersGenome.h", "sha256": "95c0de173c2a9e4a23002f456b060f349baf2f3a251fd659aa287a6393171ee0", "language": "C/C++", "lines": 63, "truncated": false, "block": 3, "row": 3671 }, { "path": "source/ParametersSolo.cpp", "sha256": "a08f59600248dbc22a593ecf19ddab5429f6432d7da5d2b7750896d3390ef1c4", "language": "C++", "lines": 721, "truncated": false, "block": 3, "row": 3255 }, { "path": "source/ParametersSolo.h", "sha256": "46558240ef417718dfbd9c2acc921ceacea9fcad9a36634ac1238794a25c53ba", "language": "C/C++", "lines": 220, "truncated": false, "block": 3, "row": 4200 }, { "path": "source/Parameters_closeReadsFiles.cpp", "sha256": "9c476fdb88bf3c370eb9445c1c19632cac18a1dcce53a87ebc7b79357f10945d", "language": "C++", "lines": 12, "truncated": false, "block": 3, "row": 716 }, { "path": "source/Parameters_openReadsFiles.cpp", "sha256": "9a868132fa48a3b9dda5e79a802abd8d6c80430b27c33e1531d26fcb1a7823cc", "language": "C++", "lines": 111, "truncated": false, "block": 3, "row": 2552 }, { "path": "source/Parameters_readFilesInit.cpp", "sha256": "d9672c1b51c578a3c2f781917c06a5820a27ffb5df498509562a4544e8c37c46", "language": "C++", "lines": 167, "truncated": false, "block": 3, "row": 2935 }, { "path": "source/Parameters_readSAMheader.cpp", "sha256": "36cb976f306358464e7b3a30099e29868656482143d2203b8f6775c9fed34eb4", "language": "C++", "lines": 44, "truncated": false, "block": 3, "row": 1699 }, { "path": "source/Parameters_samAttributes.cpp", "sha256": "8d5f074755e0e5aacaa763d079020102a178f16d3bf78f2fa9cf347b040e6b9e", "language": "C++", "lines": 263, "truncated": false, "block": 3, "row": 3063 }, { "path": "source/Quantifications.cpp", "sha256": "84563f355c50ba7b87f23812d905927ebec27f9c8d7714dd848114b7c116c88c", "language": "C++", "lines": 37, "truncated": false, "block": 3, "row": 1250 }, { "path": "source/Quantifications.h", "sha256": "7d315502780691220bf3b9e86d544caeddd56a3ef0edf82072e144197f3faba6", "language": "C/C++", "lines": 22, "truncated": false, "block": 3, "row": 3436 }, { "path": "source/ReadAlign.cpp", "sha256": "c222d7f923c57652abf3fa4cf734a86ffacd5453ccdb4fbfbcca9852d40c5b15", "language": "C++", "lines": 125, "truncated": false, "block": 3, "row": 2458 }, { "path": "source/ReadAlign.h", "sha256": "a5edf0b7b9b880eec6ea1f610fbb8c07716a855649c36c36dd0327df8534f3c4", "language": "C/C++", "lines": 239, "truncated": false, "block": 3, "row": 4309 }, { "path": "source/ReadAlignChunk.cpp", "sha256": "bce6c5cd11d3b3ddac00f21e3058945c0139c678bdf0b453ce24d55de2677537", "language": "C++", "lines": 170, "truncated": false, "block": 3, "row": 2690 }, { "path": "source/ReadAlignChunk.h", "sha256": "8a8ec5563637e49d752f1725432fd556caba4083e1fd4bbb2f0566f457550eb5", "language": "C/C++", "lines": 49, "truncated": false, "block": 3, "row": 3681 }, { "path": "source/ReadAlignChunk_mapChunk.cpp", "sha256": "e27e8ec505f05f073e16e606a04e0817e6432c60e94d04d4d3c30e6a09613b84", "language": "C++", "lines": 128, "truncated": false, "block": 3, "row": 2772 }, { "path": "source/ReadAlignChunk_processChunks.cpp", "sha256": "250c1c61a2fb9be783e5627cb4b4d776e264d754cde2cf869e46d0a579744a3a", "language": "C++", "lines": 302, "truncated": false, "block": 3, "row": 3171 }, { "path": "source/ReadAlign_CIGAR.cpp", "sha256": "d5bd49fb93f637bd36826f9ff4da1b88e63142f6ff25ac21dff2fe55416c821e", "language": "C++", "lines": 62, "truncated": false, "block": 3, "row": 2045 }, { "path": "source/ReadAlign_alignBAM.cpp", "sha256": "164bc33ddca4d8cb5057d33b1050a4b1ee6af9eb62359308e296feea9d8cdfe8", "language": "C++", "lines": 614, "truncated": false, "block": 3, "row": 3236 }, { "path": "source/ReadAlign_assignAlignToWindow.cpp", "sha256": "96a6a1ca0fa56b63e5eeb0d1f38311b52d748c0021c386aded65e087f51b1f07", "language": "C++", "lines": 130, "truncated": false, "block": 3, "row": 2568 }, { "path": "source/ReadAlign_calcCIGAR.cpp", "sha256": "3e92b38834419af1c610d8907a0624e6301ed9c83afe22ef41ff3871502d899a", "language": "C++", "lines": 58, "truncated": false, "block": 3, "row": 1889 }, { "path": "source/ReadAlign_chimericDetection.cpp", "sha256": "e83d7e5dd81150d123adeb09f7ad78839e5f2cdf9897e433faeeb4b4f3169238", "language": "C++", "lines": 57, "truncated": false, "block": 3, "row": 1741 }, { "path": "source/ReadAlign_chimericDetectionOld.cpp", "sha256": "0aaf72c4c884633df0f4059fba250799fdbd3f2f174f9c9b53bf845c159308bd", "language": "C++", "lines": 312, "truncated": false, "block": 3, "row": 3120 }, { "path": "source/ReadAlign_chimericDetectionOldOutput.cpp", "sha256": "02f91d3ed125fe6e9fa893b148e7cf71ecc33190e77b03d2144630c537767113", "language": "C++", "lines": 74, "truncated": false, "block": 3, "row": 2289 }, { "path": "source/ReadAlign_chimericDetectionPEmerged.cpp", "sha256": "edb0549cffa248837a61fc68611b6a2755b6edd60c4edad9e1276ebbc1e89af2", "language": "C++", "lines": 39, "truncated": false, "block": 3, "row": 1215 }, { "path": "source/ReadAlign_createExtendWindowsWithAlign.cpp", "sha256": "1e8e3813a066390427e12defc13004e5b678663ab16c048d097b9056b84a942d", "language": "C++", "lines": 85, "truncated": false, "block": 3, "row": 2271 }, { "path": "source/ReadAlign_mapOneRead.cpp", "sha256": "28fccbe8df679125525a783b8e84352d5e4e3edc73fa33bc0c352a07683775aa", "language": "C++", "lines": 118, "truncated": false, "block": 3, "row": 2560 }, { "path": "source/ReadAlign_mapOneReadSpliceGraph.cpp", "sha256": "228b0e5a64b44772f5ea62ebefcdbe7379211fc8ea0fbd2cc5f120379edcd5d5", "language": "C++", "lines": 40, "truncated": false, "block": 3, "row": 1278 }, { "path": "source/ReadAlign_mappedFilter.cpp", "sha256": "27e695f0b752d5e36871a1f72a081c1420f749c1a4c05e282d907e7f8ccafaf9", "language": "C++", "lines": 21, "truncated": false, "block": 3, "row": 1103 }, { "path": "source/ReadAlign_maxMappableLength2strands.cpp", "sha256": "cdff4d368b127cab3e9e3cdb3c09708940472d12f3c43fa271dbeb048f3ba6b6", "language": "C++", "lines": 115, "truncated": false, "block": 3, "row": 2497 }, { "path": "source/ReadAlign_multMapSelect.cpp", "sha256": "d4379f1b91b4100649599e256e587ca3639da88ae96cc86aa2045b45b029e9b0", "language": "C++", "lines": 95, "truncated": false, "block": 3, "row": 2336 }, { "path": "source/ReadAlign_oneRead.cpp", "sha256": "76aa9321c3cf63cc45acd8c16d0b841faec1b9b0aac3e78bbdea865867da9538", "language": "C++", "lines": 124, "truncated": false, "block": 3, "row": 2439 }, { "path": "source/ReadAlign_outputAlignments.cpp", "sha256": "fa85b7106b2aa29d1de9d9d899078f701b8c18dbeb53456b8e8f1eb663e566c7", "language": "C++", "lines": 325, "truncated": false, "block": 3, "row": 3161 }, { "path": "source/ReadAlign_outputSpliceGraphSAM.cpp", "sha256": "c0e9eec6a92039b9db44c46b8e5d6158fb4a2070e0a5788893d4ec6f8d273981", "language": "C++", "lines": 164, "truncated": false, "block": 3, "row": 2638 }, { "path": "source/ReadAlign_outputTranscriptCIGARp.cpp", "sha256": "c3316d152ebac5993a544457f27945fb1f9e194f091c53360c703f2ca3f69f6a", "language": "C++", "lines": 65, "truncated": false, "block": 3, "row": 2056 }, { "path": "source/ReadAlign_outputTranscriptSAM.cpp", "sha256": "b11673285edd158300b32ee77b20cea9890dcb4665a5c42e615113c4c35ae313", "language": "C++", "lines": 359, "truncated": false, "block": 3, "row": 3130 }, { "path": "source/ReadAlign_outputTranscriptSJ.cpp", "sha256": "57a815139cf4a0bb6912ea55a6527bebac6066729eaf345f24f1da78e95291de", "language": "C++", "lines": 56, "truncated": false, "block": 3, "row": 2191 }, { "path": "source/ReadAlign_outputVariation.cpp", "sha256": "fbebdef6f29f00e051babc9956af5cc0dc40582949d04b50c5b45950a40867fb", "language": "C++", "lines": 13, "truncated": false, "block": 3, "row": 479 }, { "path": "source/ReadAlign_peOverlapMergeMap.cpp", "sha256": "c46fe04e47192bc2792565830378a130b0a412539c8b1d204cb7355286a74fd3", "language": "C++", "lines": 368, "truncated": false, "block": 3, "row": 3095 }, { "path": "source/ReadAlign_quantTranscriptome.cpp", "sha256": "4b0816764956fb56db48d153c0f2c7176dd5aaec70ceb288fe950ea83570be65", "language": "C++", "lines": 91, "truncated": false, "block": 3, "row": 2425 }, { "path": "source/ReadAlign_stitchPieces.cpp", "sha256": "c34b9fb0705be6ed2517c921e2513e508cc5b29d7f180d9f0c3534034e8de307", "language": "C++", "lines": 350, "truncated": false, "block": 3, "row": 3117 }, { "path": "source/ReadAlign_stitchWindowSeeds.cpp", "sha256": "8cb44befc6b019ff71d91bded33db91e48229fe43e410e44dc7bc17f35d3d684", "language": "C++", "lines": 278, "truncated": false, "block": 3, "row": 3074 }, { "path": "source/ReadAlign_storeAligns.cpp", "sha256": "6352dc72a86d2a07578caf5b7710052b6274366479b53671e810d9a33398a6d1", "language": "C++", "lines": 160, "truncated": false, "block": 3, "row": 2641 }, { "path": "source/ReadAlign_transformGenome.cpp", "sha256": "e4b1a6007565ece2bb132a79473d935ef05d679aa8eed5f9521b63a8625c0c0a", "language": "C++", "lines": 74, "truncated": false, "block": 3, "row": 2128 }, { "path": "source/ReadAlign_waspMap.cpp", "sha256": "506f94281348ebabaeb257e45746c0003dabd3273a5b0141164bf363b86dfbca", "language": "C++", "lines": 128, "truncated": false, "block": 3, "row": 2353 }, { "path": "source/ReadAnnotations.h", "sha256": "86000759f930d4ae0a2b1ab1f87643398280f8ff1361b1bffef1d7d941a08603", "language": "C/C++", "lines": 47, "truncated": false, "block": 3, "row": 3714 }, { "path": "source/STAR.cpp", "sha256": "e78db2798a32c3f275c1cca717579977224e25c9e0dadba9541f3d038b8683e6", "language": "C++", "lines": 313, "truncated": false, "block": 3, "row": 3039 }, { "path": "source/SequenceFuns.cpp", "sha256": "9b0dcb17490feea51e96bbe9eac99943fda40fe04d703e1ac81343a46b59e143", "language": "C++", "lines": 445, "truncated": false, "block": 3, "row": 3126 }, { "path": "source/SequenceFuns.h", "sha256": "66f975beb0e6c9d72ca57a2957fe3601e691859e097cae91188d6932a07ec677", "language": "C/C++", "lines": 32, "truncated": false, "block": 3, "row": 3686 }, { "path": "source/SharedMemory.cpp", "sha256": "9d769797c1bd81edca8afbd6c884b1ce359017541141c243b2eab97cdc5de6eb", "language": "C++", "lines": 291, "truncated": false, "block": 3, "row": 2735 }, { "path": "source/SharedMemory.h", "sha256": "002d83da1cfb11bb859fcdb8306b1fb9f2c71359db8ffbad14e250de3fc3c5d8", "language": "C/C++", "lines": 182, "truncated": false, "block": 3, "row": 3974 }, { "path": "source/SimpleGoodTuring/sgt.h", "sha256": "2edda77c55ba4373fcce908ff0d53ad952a0ed7620d479371baa2db5edc73eee", "language": "C/C++", "lines": 300, "truncated": false, "block": 3, "row": 4353 }, { "path": "source/SjdbClass.h", "sha256": "7b7f188a241c8beeeb804e4ea44c722f966a9117cc24538ae5bf9c2a19ce98a6", "language": "C/C++", "lines": 17, "truncated": false, "block": 3, "row": 3358 }, { "path": "source/Solo.cpp", "sha256": "33f059b629c62b91d06f7c365e9cf7f9be917e6e08064b933b40fa171a430939", "language": "C++", "lines": 91, "truncated": false, "block": 3, "row": 2183 }, { "path": "source/Solo.h", "sha256": "311e77d3f576e63fe335ff1a200bd750e523c0ec86a0a97803a0aec9377b6e7d", "language": "C/C++", "lines": 30, "truncated": false, "block": 3, "row": 3423 }, { "path": "source/SoloBarcode.cpp", "sha256": "da84f5a70b9ae7665de854554dee7ddbf11889862d122acd25d6fe374c7cd667", "language": "C++", "lines": 152, "truncated": false, "block": 3, "row": 2722 }, { "path": "source/SoloBarcode.h", "sha256": "90fb66c769d23e8d4b66c581f7f5805f06574526171f465565141895ca4cdb25", "language": "C/C++", "lines": 38, "truncated": false, "block": 3, "row": 3596 }, { "path": "source/SoloBarcode_extractBarcode.cpp", "sha256": "a0553205134146a0081f4aaf1510a492ad21d012d60d74ae60cc5ed13563e137", "language": "C++", "lines": 34, "truncated": false, "block": 3, "row": 1257 }, { "path": "source/SoloCommon.h", "sha256": "93868869b5e66d8ab94e7aba97e2e5adcc01d09786025d1590e254e144405a6b", "language": "C/C++", "lines": 80, "truncated": false, "block": 3, "row": 3824 }, { "path": "source/SoloFeature.cpp", "sha256": "f3a7443a1fdb849d652048fba0e01b1f1bab634575874a9b427d3836083ac883", "language": "C++", "lines": 65, "truncated": false, "block": 3, "row": 1859 }, { "path": "source/SoloFeature.h", "sha256": "4185cb5055d5519c87cf5a68a7f65acc73ae3fa25d31dc428148f645ff4134c7", "language": "C/C++", "lines": 110, "truncated": false, "block": 3, "row": 4022 }, { "path": "source/SoloFeatureTypes.h", "sha256": "5f7d2bb2ea1eec942115271fa6ea5479740fecd2877672593aa9cbe739dd4efe", "language": "C/C++", "lines": 12, "truncated": false, "block": 3, "row": 3434 }, { "path": "source/SoloFeature_addBAMtags.cpp", "sha256": "a82e844594127424fdf29a20936906132e12e4624966784f998cca1746e81e12", "language": "C++", "lines": 26, "truncated": false, "block": 3, "row": 1039 }, { "path": "source/SoloFeature_cellFiltering.cpp", "sha256": "5134339f861572cee4c329004169babe803cda181fa2dad60f7c59be5b10a034", "language": "C++", "lines": 131, "truncated": false, "block": 3, "row": 2648 }, { "path": "source/SoloFeature_collapseUMI_Graph.cpp", "sha256": "b35965f41bd65fb8124876a595fb0a50277014ad11d65f035ad115477d7b3aac", "language": "C++", "lines": 172, "truncated": false, "block": 3, "row": 2793 }, { "path": "source/SoloFeature_collapseUMIall.cpp", "sha256": "d2cfbafa3bc933b55b3b2cb55860811c65a0b9863e2290958aae920bda6be295", "language": "C++", "lines": 658, "truncated": false, "block": 3, "row": 3238 }, { "path": "source/SoloFeature_countCBgeneUMI.cpp", "sha256": "ae124ffba531e2bcc56d5a9386916aed5a4b43ab29ec9a813936449bcc8dbacf", "language": "C++", "lines": 112, "truncated": false, "block": 3, "row": 2471 }, { "path": "source/SoloFeature_countSmartSeq.cpp", "sha256": "a23b5dbb34dd35cfc793831be1131fb4a43efba5d7db8821f05fe53a590cd383", "language": "C++", "lines": 159, "truncated": false, "block": 3, "row": 2701 }, { "path": "source/SoloFeature_countVelocyto.cpp", "sha256": "d99af8573a5f4d2eed3b1591dda48a426f021c2164335bc05ee0137c5a7c82f5", "language": "C++", "lines": 166, "truncated": false, "block": 3, "row": 2823 }, { "path": "source/SoloFeature_emptyDrops_CR.cpp", "sha256": "4dbbefadc28ff21cee5f6ab3c656d3001bfbf75c0585b140ed297fa73275570c", "language": "C++", "lines": 231, "truncated": false, "block": 3, "row": 3016 }, { "path": "source/SoloFeature_loadRawMatrix.cpp", "sha256": "d736d66ccb848f086e3b731b003538095345b1b2778627026efe7a86dc0c5d90", "language": "C++", "lines": 141, "truncated": false, "block": 3, "row": 2673 }, { "path": "source/SoloFeature_outputResults.cpp", "sha256": "1797225698f0ce551b70e3fc76914cf41aa1e59a721b14bc592a24708d5b0653", "language": "C++", "lines": 241, "truncated": false, "block": 3, "row": 3036 }, { "path": "source/SoloFeature_processRecords.cpp", "sha256": "56e8735464c69ecc23fb9368836766293693dc0ec32b152913d401660b604861", "language": "C++", "lines": 87, "truncated": false, "block": 3, "row": 2174 }, { "path": "source/SoloFeature_quantTranscript.cpp", "sha256": "993bf1445a2fb03a0181882c83d2e1cd6481c8c20f83b611e2453d6c53390df2", "language": "C++", "lines": 327, "truncated": false, "block": 3, "row": 3133 }, { "path": "source/SoloFeature_redistributeReadsByCB.cpp", "sha256": "b3b182331e601bef19b8d1ca116cf38c1924a7cdee05ba017027011952d1b821", "language": "C++", "lines": 80, "truncated": false, "block": 3, "row": 2066 }, { "path": "source/SoloFeature_statsOutput.cpp", "sha256": "46ddede74e503aaed0c5cbd5b3f053b8423f5a064bee5464b76ff655b5db10f5", "language": "C++", "lines": 123, "truncated": false, "block": 3, "row": 2631 }, { "path": "source/SoloFeature_sumThreads.cpp", "sha256": "d8e55e4434f192f6fd000f7241921729cc3088030a17ec61c923ecbac6a563db", "language": "C++", "lines": 101, "truncated": false, "block": 3, "row": 2320 }, { "path": "source/SoloFilteredCells.h", "sha256": "bc7e7d0a6cb2411b653c98b6e3694d3e31e95723c0fe0ea09d41eddb91a92c6a", "language": "C/C++", "lines": 33, "truncated": false, "block": 3, "row": 3499 }, { "path": "source/SoloRead.cpp", "sha256": "874a73ea609d25d58df320463332b70b6425756951b72d927e8f897f37594a47", "language": "C++", "lines": 22, "truncated": false, "block": 3, "row": 845 }, { "path": "source/SoloRead.h", "sha256": "9526d0b122400bd0358a66d1ecbd7c654b6d6070e8e203173f506a5ad0350d36", "language": "C/C++", "lines": 23, "truncated": false, "block": 3, "row": 3410 }, { "path": "source/SoloReadBarcode.cpp", "sha256": "3913a9b1420401758758990d757e5ac443bf6a748aba5b5f42f5b239db20fe34", "language": "C++", "lines": 51, "truncated": false, "block": 3, "row": 1389 }, { "path": "source/SoloReadBarcode.h", "sha256": "968775590bc37f3f73174a48d14a3a8289ae4801db47a1d24a7260a4b6b70825", "language": "C/C++", "lines": 46, "truncated": false, "block": 3, "row": 3667 }, { "path": "source/SoloReadBarcodeStats.h", "sha256": "d3e6302d6809b8858e78ec5a8ac7fd0d18e0c087f55c275d79ceb74061f2528f", "language": "C/C++", "lines": 27, "truncated": false, "block": 3, "row": 3479 }, { "path": "source/SoloReadBarcode_getCBandUMI.cpp", "sha256": "7fa473b91b86a1092b942eed68e6d408fe988a9005351a01e35b088bfa476508", "language": "C++", "lines": 429, "truncated": false, "block": 3, "row": 3178 }, { "path": "source/SoloReadFeature.cpp", "sha256": "8132da88c6fe520c1b11200fae2e857867ac0c00ea7acd4923b50d7a8a1db52c", "language": "C++", "lines": 63, "truncated": false, "block": 3, "row": 1770 }, { "path": "source/SoloReadFeature.h", "sha256": "90493c8290bcff5bd71e47d22b2b863fd62dad716f262c14b4462d146c8a0b9c", "language": "C/C++", "lines": 50, "truncated": false, "block": 3, "row": 3609 }, { "path": "source/SoloReadFeatureStats.h", "sha256": "de58cf487ec32ac3e5bfed8669ed590893e8b4425647a820d4ce3a58c6c6eea8", "language": "C/C++", "lines": 49, "truncated": false, "block": 3, "row": 3691 }, { "path": "source/SoloReadFeature_inputRecords.cpp", "sha256": "02005bd7e8c86ed9607847a908d0f6a5b5c70c99145c348b09d9aec35aba22e7", "language": "C++", "lines": 172, "truncated": false, "block": 3, "row": 2790 }, { "path": "source/SoloReadFeature_record.cpp", "sha256": "32d85312e9044fc10d3015bc7b478bc535eeb9bd779c904e3e9fbc58610c2f35", "language": "C++", "lines": 276, "truncated": false, "block": 3, "row": 3079 }, { "path": "source/SoloRead_record.cpp", "sha256": "a9c799e889d65a1fd926aab68bb418c920fbefbdbacfc35250c4e343e2c8b372", "language": "C++", "lines": 15, "truncated": false, "block": 3, "row": 751 }, { "path": "source/SpliceGraph.cpp", "sha256": "c96dac9d20cd090e66e8ea9c8c13989e6ce629eaf827c00194f81181ae3420b7", "language": "C++", "lines": 33, "truncated": false, "block": 3, "row": 1219 }, { "path": "source/SpliceGraph.h", "sha256": "ba0723cffbde74d492a5056e91685344d826204db2c31c245649f21eddbf61ef", "language": "C/C++", "lines": 58, "truncated": false, "block": 3, "row": 3715 }, { "path": "source/SpliceGraph_findSuperTr.cpp", "sha256": "ac4d2549cb32c321df610a08baf699929cda7a3bb912549ca270a2dee45bf4a5", "language": "C++", "lines": 186, "truncated": false, "block": 3, "row": 2864 }, { "path": "source/SpliceGraph_swScoreSpliced.cpp", "sha256": "d9c824fa6143ce22d53e281cda9fee1b813af98308060eb9387611242da1393a", "language": "C++", "lines": 249, "truncated": false, "block": 3, "row": 2963 }, { "path": "source/SpliceGraph_swTraceBack.cpp", "sha256": "a8b27ec4c182a7ea9d7501dd9ab8ede438216a64cc91475f778a639c155484ef", "language": "C++", "lines": 19, "truncated": false, "block": 3, "row": 833 }, { "path": "source/Stats.cpp", "sha256": "8120977869f2360d1486f3f5f3e52e6032f53ce255e569ac86026047fa12f92f", "language": "C++", "lines": 156, "truncated": false, "block": 3, "row": 2941 }, { "path": "source/Stats.h", "sha256": "ec5029ae0b7e7ca5798525b836b42ac93b7d3ef99d6f134a36fd6495c75ce16a", "language": "C/C++", "lines": 41, "truncated": false, "block": 3, "row": 3680 }, { "path": "source/SuffixArrayFuns.cpp", "sha256": "3e33a7568fb181fdad65fce125f818aa18634f5c33a8c44dca45a567ff3b31ff", "language": "C++", "lines": 410, "truncated": false, "block": 3, "row": 3068 }, { "path": "source/SuffixArrayFuns.h", "sha256": "f35e70b6359a919b9adccf3cb6f625a0ba6c8344098526fd637f4c84b58af710", "language": "C/C++", "lines": 18, "truncated": false, "block": 3, "row": 3483 }, { "path": "source/SuperTranscriptome.cpp", "sha256": "c38b97c33fe410d93b33d973f36b73b1b1dc0e78d1da2e2ff07b0435ee8cbe94", "language": "C++", "lines": 92, "truncated": false, "block": 3, "row": 2297 }, { "path": "source/SuperTranscriptome.h", "sha256": "4a04370dc22e9d26c1756412906221d8c1c99161669b2060dd4d9ae42ba8429a", "language": "C/C++", "lines": 42, "truncated": false, "block": 3, "row": 3565 }, { "path": "source/ThreadControl.cpp", "sha256": "36cca68786a85a7a336554d9dd6b78b3830de1f47dd6b88b559eb68b4288b3af", "language": "C++", "lines": 7, "truncated": false, "block": 3, "row": 475 }, { "path": "source/ThreadControl.h", "sha256": "966eb9cc9b166a598e4c0853ea8ec07b6cbb438e75d5582485fc2982593d29c6", "language": "C/C++", "lines": 29, "truncated": false, "block": 3, "row": 3437 }, { "path": "source/TimeFunctions.cpp", "sha256": "b00ba65f0831defa4a84ec8eff06af2d0d806af312354f6f8d1ef9b01daaf19c", "language": "C++", "lines": 20, "truncated": false, "block": 3, "row": 846 }, { "path": "source/TimeFunctions.h", "sha256": "fe4af9be5d3872145195d45b33ea44234b36123c34b723eef5094558fdbdad81", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3333 }, { "path": "source/Transcript.cpp", "sha256": "4fca46a05cf57ce222699e570c41f275a7d75a1d4bd4c9a34a6fa062cd90b9c8", "language": "C++", "lines": 59, "truncated": false, "block": 3, "row": 1575 }, { "path": "source/Transcript.h", "sha256": "a5e3c904966d1b3d23084a8543b6497d495bc767f77969772c7294fd71efbc86", "language": "C/C++", "lines": 83, "truncated": false, "block": 3, "row": 3907 }, { "path": "source/Transcript_alignScore.cpp", "sha256": "0188598f8fe151d39dfb0e28ae8c4d7776251fd312321adc483ba7bf24094e92", "language": "C++", "lines": 60, "truncated": false, "block": 3, "row": 1839 }, { "path": "source/Transcript_convertGenomeCigar.cpp", "sha256": "0f75b8de539502d8be1984badc5818454c6f021dbbb799f17da5ea4a3c4013f5", "language": "C++", "lines": 161, "truncated": false, "block": 3, "row": 2721 }, { "path": "source/Transcript_generateCigarP.cpp", "sha256": "bcd1d502a1c60a3abe74df0d860d667778b2af878f60d557965328ff532d3833", "language": "C++", "lines": 63, "truncated": false, "block": 3, "row": 1990 }, { "path": "source/Transcript_transformGenome.cpp", "sha256": "c4dbd9342ab970d9bc345f130fcfc11c839335931c40153b410ec6a2c46d9019", "language": "C++", "lines": 167, "truncated": false, "block": 3, "row": 2739 }, { "path": "source/Transcript_variationAdjust.cpp", "sha256": "c8d8869163604efedd36bf36b779e3fa3241def43982702e91a3e40fd9cefe41", "language": "C++", "lines": 74, "truncated": false, "block": 3, "row": 1884 }, { "path": "source/Transcript_variationOutput.cpp", "sha256": "69eb6a8b6a64a6837bb743ce3252fe580da5c2bf59d60937f12d0820cf53bf60", "language": "C++", "lines": 6, "truncated": false, "block": 3, "row": 449 }, { "path": "source/Transcriptome.cpp", "sha256": "ae4cc400fc192a39ea1e8e362649fb77d34d7a9eff91261254be3624258ac4db", "language": "C++", "lines": 190, "truncated": false, "block": 3, "row": 2789 }, { "path": "source/Transcriptome.h", "sha256": "eb91787a6c0f7869893fa0dd6d80f26c9c782af0cab238e2048183e8e2310173", "language": "C/C++", "lines": 63, "truncated": false, "block": 3, "row": 3854 }, { "path": "source/Transcriptome_alignExonOverlap.cpp", "sha256": "458c2118847938b4dc0c4e4bb4ace44575270c8f8e0f40cc77a025eceeac41cc", "language": "C++", "lines": 278, "truncated": false, "block": 3, "row": 3005 }, { "path": "source/Transcriptome_classifyAlign.cpp", "sha256": "447a9dfe2ccccffc48a90ced90198962756c077164321c5122548a6649be0bcb", "language": "C++", "lines": 267, "truncated": false, "block": 3, "row": 3076 }, { "path": "source/Transcriptome_geneCountsAddAlign.cpp", "sha256": "c5fdc5ac5a8d3bc55518093439a7fefa51c2c18eed013a08d61ea5a776a4dc9c", "language": "C++", "lines": 63, "truncated": false, "block": 3, "row": 2021 }, { "path": "source/Transcriptome_geneFullAlignOverlap.cpp", "sha256": "f14abf6f94645d69f10cafa1d9b27bfbe1ccd2f1f6f84b9a54324963ea4cadbc", "language": "C++", "lines": 56, "truncated": false, "block": 3, "row": 1895 }, { "path": "source/Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp", "sha256": "1d8412c4e189db492117a1a624718f87acebd7e2fb636d50d1f27fe409685565", "language": "C++", "lines": 43, "truncated": false, "block": 3, "row": 1716 }, { "path": "source/Transcriptome_quantAlign.cpp", "sha256": "0deb0526f49394d92d2be22857a7c7a0632129f066fdaadcc621343996570e5b", "language": "C++", "lines": 114, "truncated": false, "block": 3, "row": 2564 }, { "path": "source/Variation.cpp", "sha256": "90528f56ff60b117003e63d27bac3e485bd9d6f74e660a07264490da34e2fd7e", "language": "C++", "lines": 157, "truncated": false, "block": 3, "row": 2695 }, { "path": "source/Variation.h", "sha256": "15b097ed4b10486856e028e0fb5bc68483384d4cb0a22444c557d26d32ea7c0e", "language": "C/C++", "lines": 53, "truncated": false, "block": 3, "row": 3644 }, { "path": "source/bamRemoveDuplicates.cpp", "sha256": "f1556e188766a9d21c79bcca2ac9bb4db8c4f83aefec2c3ffcd324e4beefcf48", "language": "C++", "lines": 271, "truncated": false, "block": 3, "row": 3012 }, { "path": "source/bamRemoveDuplicates.h", "sha256": "59a3b90a6aa438a291353717112b741d68438bfe6dfbf7ece44585c433418f60", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3346 }, { "path": "source/bamSortByCoordinate.cpp", "sha256": "d9aa60ea1ae0034911a09f177f89e20d7aac32282e3ee72aed67f28107bcc359", "language": "C++", "lines": 97, "truncated": false, "block": 3, "row": 2487 }, { "path": "source/bamSortByCoordinate.h", "sha256": "cebc4ef31bd324ad24609958f8be3c77c9984ef3fabb65c3bf5cdd7b2bfa1721", "language": "C/C++", "lines": 11, "truncated": false, "block": 3, "row": 3356 }, { "path": "source/bam_cat.c", "sha256": "8ceb77529243c3c0738dd027630b94924756ac7b6d434d907edb7498fc509a2f", "language": "C", "lines": 143, "truncated": false, "block": 3, "row": 128 }, { "path": "source/bam_cat.h", "sha256": "d730a66e4059292b7fc2d00b4666facb3eb28637a89fef8754ba6189f7f2ebc7", "language": "C/C++", "lines": 8, "truncated": false, "block": 3, "row": 3329 }, { "path": "source/binarySearch2.cpp", "sha256": "f793e8bca4d26019727865c8145d1018839c34ce41a495787557bf7843217a50", "language": "C++", "lines": 43, "truncated": false, "block": 3, "row": 1122 }, { "path": "source/binarySearch2.h", "sha256": "1e6c025ec01771c966ee3773472a440e34e77dad07b5be9d542d05adea3a6af7", "language": "C/C++", "lines": 7, "truncated": false, "block": 3, "row": 3327 }, { "path": "source/blocksOverlap.cpp", "sha256": "cd232640757e849b419db19d127548375b48dfdb8330b31edda63e4e5b3cbdb1", "language": "C++", "lines": 41, "truncated": false, "block": 3, "row": 1427 }, { "path": "source/blocksOverlap.h", "sha256": "359b6936ed394acbb6b3439b3cc4bdc97c6ba58ce48f6c4c49541620bd0c8e19", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3332 }, { "path": "source/extendAlign.cpp", "sha256": "1aa080441241c4ceb59ed7893a2b7b020b47b85683e41ab18bc27a1df6d69213", "language": "C++", "lines": 93, "truncated": false, "block": 3, "row": 1952 }, { "path": "source/extendAlign.h", "sha256": "dd2e1f549c4cb00a4c482ecc812046b8839f97a14b44ceba19c5826b778c3368", "language": "C/C++", "lines": 6, "truncated": false, "block": 3, "row": 3355 }, { "path": "source/funCompareUintAndSuffixes.cpp", "sha256": "e0f8f2444d36f3e07405d1f64267030a9ab255c52c9dc5df4db9b10b124b53a4", "language": "C++", "lines": 40, "truncated": false, "block": 3, "row": 1431 }, { "path": "source/funCompareUintAndSuffixes.h", "sha256": "cf7548918f72949df43f894df79dbcb97c4169907cb5b4248637cfc84d48a420", "language": "C/C++", "lines": 11, "truncated": false, "block": 3, "row": 3357 }, { "path": "source/funCompareUintAndSuffixesMemcmp.cpp", "sha256": "2ba6cf2880e039e2da812adad6e44a4216ad791035f83650b03de91f08e0e28d", "language": "C++", "lines": 33, "truncated": false, "block": 3, "row": 1335 }, { "path": "source/funCompareUintAndSuffixesMemcmp.h", "sha256": "1dfffd61f5553d0c0d49589d0a6984b70855c5e23d654fd0ac7b6e33df04b6af", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3367 }, { "path": "source/funPrimaryAlignMark.cpp", "sha256": "19d23ed8a6eb88ef2bbe8b2160222b0e6f10dfcd4741657a424d7dc3c996f969", "language": "C++", "lines": 43, "truncated": false, "block": 3, "row": 1795 }, { "path": "source/funPrimaryAlignMark.h", "sha256": "fb971da7701cf692cb4ff72e0fc2db3d55cd9f38df218e1897e3946d4de608c9", "language": "C/C++", "lines": 5, "truncated": false, "block": 3, "row": 3354 }, { "path": "source/genomeGenerate.h", "sha256": "abbe731b99b1de32bce2a8b899ee384f008c71883f3b144d4d36131b463cacae", "language": "C/C++", "lines": 4, "truncated": false, "block": 3, "row": 3319 }, { "path": "source/genomeParametersWrite.cpp", "sha256": "58c6c41029ef72c46adec18e797272a8b4e9255c98b27c866af3852025b6ebda", "language": "C++", "lines": 45, "truncated": false, "block": 3, "row": 1818 }, { "path": "source/genomeParametersWrite.h", "sha256": "00b4452e9b7191c305f31aac6c458110e9277077e3804645745fd901ca63ab85", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3342 }, { "path": "source/genomeSAindex.cpp", "sha256": "668659d86c76e26e8ea4dd1049f50fc3751f495b8926a8e218d2825a39daffa2", "language": "C++", "lines": 217, "truncated": false, "block": 3, "row": 2887 }, { "path": "source/genomeSAindex.h", "sha256": "c2d72c445f4d691ca4bd62f1a28d36076cfd54497db9caf4983faaba22da5ade", "language": "C/C++", "lines": 11, "truncated": false, "block": 3, "row": 3409 }, { "path": "source/genomeScanFastaFiles.cpp", "sha256": "313eab6f7bdc19049c5e90bcc25b8ee0e87d7d466eff7dc61900788017720193", "language": "C++", "lines": 92, "truncated": false, "block": 3, "row": 2375 }, { "path": "source/genomeScanFastaFiles.h", "sha256": "576c9875252f06533361d031fd6896cd82150ae79916120cc3dfcdc41259f4e3", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3344 }, { "path": "source/htslib/bgzf.c", "sha256": "27871beb0e540f1e13921f781af079f94a818e20c1c9acea3ea1031b3a7e7684", "language": "C", "lines": 1085, "truncated": false, "block": 3, "row": 309 }, { "path": "source/htslib/bgzip.c", "sha256": "346422dd9abb2a00ddd34bcc2ad37a061254dea4451ab78451aa731d2d27635b", "language": "C", "lines": 283, "truncated": false, "block": 3, "row": 221 }, { "path": "source/htslib/config.h", "sha256": "84eb607a340a356e7bc8a88992b505277c103bd7e1746880800154a44e8682c3", "language": "C/C++", "lines": 3, "truncated": false, "block": 3, "row": 3318 }, { "path": "source/htslib/cram/cram.h", "sha256": "60cbfd6f7d39df134c1256457d554d7a1b9d09c7fafb168c07ee1c3b238a0e88", "language": "C/C++", "lines": 66, "truncated": false, "block": 3, "row": 3845 }, { "path": "source/htslib/cram/cram_codecs.c", "sha256": "06b5f71b248a5ae943f793922185aa2366350456d7afeda2f9f3485b0ce286d3", "language": "C", "lines": 1764, "truncated": false, "block": 3, "row": 320 }, { "path": "source/htslib/cram/cram_codecs.h", "sha256": "aa9ba7e4ca7251326bd1f042b69627d3d2fce76c5e8044389a4b71a13274e618", "language": "C/C++", "lines": 155, "truncated": false, "block": 3, "row": 4075 }, { "path": "source/htslib/cram/cram_decode.c", "sha256": "569a2c861c3d53e9c42db54fc91f9da2d09bc251579b94611c56d1890aa3a0e6", "language": "C", "lines": 2138, "truncated": false, "block": 3, "row": 326 }, { "path": "source/htslib/cram/cram_decode.h", "sha256": "0e725c07424d8ae991e10739e15abaac93e1965c71c57b1f8192bc9e0a7b2e2a", "language": "C/C++", "lines": 112, "truncated": false, "block": 3, "row": 3975 }, { "path": "source/htslib/cram/cram_encode.c", "sha256": "41d9758226a547ba4d6296e32e05345c8b09512874d4afbb889494ba610d9bb1", "language": "C", "lines": 2630, "truncated": false, "block": 3, "row": 330 }, { "path": "source/htslib/cram/cram_encode.h", "sha256": "5554c37504d4ce1c0681fce5a573513212d5e043e1217aca844b2a583465537d", "language": "C/C++", "lines": 105, "truncated": false, "block": 3, "row": 3951 }, { "path": "source/htslib/cram/cram_index.c", "sha256": "72ebd8c444c65326dc5c637586c34977999037e58714712c74e6a6fe7f9257e1", "language": "C", "lines": 503, "truncated": false, "block": 3, "row": 253 }, { "path": "source/htslib/cram/cram_index.h", "sha256": "7666b6941ffd809fc91320519cfdaf05a60c22c443c59898e12c7243b8d9843d", "language": "C/C++", "lines": 98, "truncated": false, "block": 3, "row": 3940 }, { "path": "source/htslib/cram/cram_io.c", "sha256": "39839fc3a3eefe63d3579129aad8747f46e23cb53ca76f2d0a57209ed5d8d989", "language": "C", "lines": 3652, "truncated": false, "block": 3, "row": 337 }, { "path": "source/htslib/cram/cram_io.h", "sha256": "e6d849d73deb75e56e661f26e34cb3e29f3de44aa260578d7a0c2dce33dbfca8", "language": "C/C++", "lines": 532, "truncated": false, "block": 3, "row": 4446 }, { "path": "source/htslib/cram/cram_samtools.c", "sha256": "38e64fe182fb228e03b482d5e86a84b1dbbafe3303c491e8538178bc18e824f8", "language": "C", "lines": 144, "truncated": false, "block": 3, "row": 131 }, { "path": "source/htslib/cram/cram_samtools.h", "sha256": "10e30fc368e34fef90ba819c7fce84882936b8d9af8a90e18bb62ee4dc4b2042", "language": "C/C++", "lines": 97, "truncated": false, "block": 3, "row": 3971 }, { "path": "source/htslib/cram/cram_stats.c", "sha256": "07168d5a426724d7961ec60d7ac9c91324541337cc7019709bf7f6d5a0b04648", "language": "C", "lines": 357, "truncated": false, "block": 3, "row": 227 }, { "path": "source/htslib/cram/cram_stats.h", "sha256": "ce86e85c2aa3931ac0ab6f9be7e9964ad0bda7a6f70b6745b897b2e90c20b3ab", "language": "C/C++", "lines": 59, "truncated": false, "block": 3, "row": 3844 }, { "path": "source/htslib/cram/cram_structs.h", "sha256": "2d29eba8edab9f17b9588ffac43cc051f7771bfb0a7ab536232598cca023c77c", "language": "C/C++", "lines": 752, "truncated": false, "block": 3, "row": 4531 }, { "path": "source/htslib/cram/files.c", "sha256": "8957b94a2db8218ab97848510c973453f56927478f0a5b64fc100698fc22d358", "language": "C", "lines": 76, "truncated": false, "block": 3, "row": 72 }, { "path": "source/htslib/cram/mFILE.c", "sha256": "9a5264a3b538e3e19d4d15721fce3b2e9f288576d4e0c7d939b5df9aee92a39a", "language": "C", "lines": 634, "truncated": false, "block": 3, "row": 272 }, { "path": "source/htslib/cram/mFILE.h", "sha256": "a89fe6b07c2a0abbd9bf58b11d4d38dca385923eff8a972e49c470089dc8b489", "language": "C/C++", "lines": 88, "truncated": false, "block": 3, "row": 3919 }, { "path": "source/htslib/cram/md5.c", "sha256": "dceae37d45d1230b13e9269aa6269b68894aae066db389a0161921939d231802", "language": "C", "lines": 295, "truncated": false, "block": 3, "row": 212 }, { "path": "source/htslib/cram/md5.h", "sha256": "b48b94d9a3274588cc0d1b1fbe1cca840ca6e70633857212617f676166dd06ec", "language": "C/C++", "lines": 54, "truncated": false, "block": 3, "row": 3668 }, { "path": "source/htslib/cram/misc.h", "sha256": "920d1b1236f6fd855f490bb82e8fc9dd3907f9c0d4db642cc7c6334b3dbcc11e", "language": "C/C++", "lines": 110, "truncated": false, "block": 3, "row": 4039 }, { "path": "source/htslib/cram/open_trace_file.c", "sha256": "5f449051460fda5b392670dc0f6724f2b8f8ef9236d888ac717f959311839271", "language": "C", "lines": 386, "truncated": false, "block": 3, "row": 242 }, { "path": "source/htslib/cram/open_trace_file.h", "sha256": "9a38ed161ee98c6b597fa692293771de30ffa04822088928b9b94d97c4b72924", "language": "C/C++", "lines": 115, "truncated": false, "block": 3, "row": 4070 }, { "path": "source/htslib/cram/os.h", "sha256": "66a73e185c901fa3e7977666c4a30b206117fea1a741bdc3c09aa1ec72bdaaab", "language": "C/C++", "lines": 306, "truncated": false, "block": 3, "row": 4312 }, { "path": "source/htslib/cram/pooled_alloc.c", "sha256": "a71072ac81709b2c320560d0d894935f5b1d21c30c670a5befe0a77c4412db31", "language": "C", "lines": 170, "truncated": false, "block": 3, "row": 115 }, { "path": "source/htslib/cram/pooled_alloc.h", "sha256": "9a30517982d6ec7dbb31d8b95472901dea374b2f96e78b95847b6bf6af7993ec", "language": "C/C++", "lines": 56, "truncated": false, "block": 3, "row": 3811 }, { "path": "source/htslib/cram/sam_header.c", "sha256": "4cc82311770e493669796a1f99701cff5df011e12ed715e156e65262f4a2e63f", "language": "C", "lines": 1222, "truncated": false, "block": 3, "row": 306 }, { "path": "source/htslib/cram/sam_header.h", "sha256": "eca37855be63b131aef1351065505d60d8a6e5bfde65d38c5985edee4bd1c439", "language": "C/C++", "lines": 452, "truncated": false, "block": 3, "row": 4422 }, { "path": "source/htslib/cram/string_alloc.c", "sha256": "0e6be70eaf51078638ff691ac15fc0ba08b9172a33bfe75e6024aaf880cc0446", "language": "C", "lines": 153, "truncated": false, "block": 3, "row": 114 }, { "path": "source/htslib/cram/string_alloc.h", "sha256": "df1cfcc4e6c799ae462377adfe89182c1b9bec8461d007e4161ad98b0177741b", "language": "C/C++", "lines": 69, "truncated": false, "block": 3, "row": 3847 }, { "path": "source/htslib/cram/thread_pool.c", "sha256": "9ac9938630b94becfdfadf1e556f01975bdf93439d4a846750b5bb5a49b57c0d", "language": "C", "lines": 713, "truncated": false, "block": 3, "row": 275 }, { "path": "source/htslib/cram/thread_pool.h", "sha256": "b30170badc7b0088ac2ba51d4ec925f1af207e7b5f36c3d02366b74b0b1138de", "language": "C/C++", "lines": 197, "truncated": false, "block": 3, "row": 4165 }, { "path": "source/htslib/cram/vlen.c", "sha256": "a8ddd7f2e9f4e6965d8212f2bf587ed37c012e5dcf00332f5fd3377b81d4d79a", "language": "C", "lines": 432, "truncated": false, "block": 3, "row": 250 }, { "path": "source/htslib/cram/vlen.h", "sha256": "c64ffb293343f03b5c24bce87557e344c2e28efdebf6cd62ecbed03c68bae05a", "language": "C/C++", "lines": 48, "truncated": false, "block": 3, "row": 3755 }, { "path": "source/htslib/cram/zfio.c", "sha256": "7c6867443ee4940d86dce4cb5f25b757d5393b4c55cfd3581e70aed70df7490e", "language": "C", "lines": 185, "truncated": false, "block": 3, "row": 135 }, { "path": "source/htslib/cram/zfio.h", "sha256": "444f5917a615bb560ded533b1798536dcc912598a02b03579a22897fb7e056ca", "language": "C/C++", "lines": 54, "truncated": false, "block": 3, "row": 3807 }, { "path": "source/htslib/faidx.c", "sha256": "d28f3109cee85870bb29d48d487c3460cb7f75f2bb5de91da443dcfba5f87bee", "language": "C", "lines": 421, "truncated": false, "block": 3, "row": 240 }, { "path": "source/htslib/hfile.c", "sha256": "f235267649b1fae420ec58b93ea59e474dcfdfc311de39316be09c630c00a27a", "language": "C", "lines": 526, "truncated": false, "block": 3, "row": 264 }, { "path": "source/htslib/hfile_internal.h", "sha256": "70fc91f4844cc7ee3db62a1a7042faa154c5c0fc624e15290fa1e7a58dda4e58", "language": "C/C++", "lines": 75, "truncated": false, "block": 3, "row": 3978 }, { "path": "source/htslib/hfile_net.c", "sha256": "52e4f23a77a1a7d83caf1d1b905fc6330509ae338e0519b85a98953c5db36812", "language": "C", "lines": 99, "truncated": false, "block": 3, "row": 86 }, { "path": "source/htslib/hts.c", "sha256": "65817d5ea8b25ab7249432d12d98316c08a76a79fdab973705b62d5bb8b888dd", "language": "C", "lines": 1326, "truncated": false, "block": 3, "row": 315 }, { "path": "source/htslib/htslib/bgzf.h", "sha256": "9638516c0496f19347ff33101b581e6a90e24d185b41679a81de0c23d5e35568", "language": "C/C++", "lines": 313, "truncated": false, "block": 3, "row": 4321 }, { "path": "source/htslib/htslib/faidx.h", "sha256": "f617f16520c0ac65fab5348c784fbba53cacfea8be5750f9f1df75de9526bc9c", "language": "C/C++", "lines": 112, "truncated": false, "block": 3, "row": 3996 }, { "path": "source/htslib/htslib/hfile.h", "sha256": "6c7632b5e2d0b62ab17fa908b01877259d7ab8f294967afda9dd56b5ca77fd90", "language": "C/C++", "lines": 204, "truncated": false, "block": 3, "row": 4179 }, { "path": "source/htslib/htslib/hts.h", "sha256": "26d9a2fc09d6a347d8a96fa6351aa062d232d3ef51fbc1d8bff60d9bf3f30709", "language": "C/C++", "lines": 305, "truncated": false, "block": 3, "row": 4306 }, { "path": "source/htslib/htslib/hts_defs.h", "sha256": "4277eefdcef61c83dad25af674f6f194fdacefd964fd171d7bfabd03b6ce3c1e", "language": "C/C++", "lines": 47, "truncated": false, "block": 3, "row": 3728 }, { "path": "source/htslib/htslib/kfunc.h", "sha256": "a3ee46dbb9957217e1d43d024de4a45f5b42459066c0a819e3016ecbea3c9160", "language": "C/C++", "lines": 49, "truncated": false, "block": 3, "row": 3652 }, { "path": "source/htslib/htslib/khash.h", "sha256": "41e778a9b0d79addccb83263667533ff2af81a8836da7edc6160dfade150968a", "language": "C/C++", "lines": 617, "truncated": false, "block": 3, "row": 4527 }, { "path": "source/htslib/htslib/khash_str2int.h", "sha256": "26d38be1be71bf8c8568b2f3d213e6bbcbd26184aa498de6f67cf87b2710da19", "language": "C/C++", "lines": 98, "truncated": false, "block": 3, "row": 3859 }, { "path": "source/htslib/htslib/klist.h", "sha256": "47368e3dd36028d096bc5106d31bd097f360b3b5e58f0c785f383c1adc53317a", "language": "C/C++", "lines": 121, "truncated": false, "block": 3, "row": 4063 }, { "path": "source/htslib/htslib/knetfile.h", "sha256": "c874934128c551fc0bc9bbe65d4605cf537780ac088c458687b572fd4eec42e7", "language": "C/C++", "lines": 75, "truncated": false, "block": 3, "row": 3701 }, { "path": "source/htslib/htslib/kseq.h", "sha256": "bee65d55a4910f51966188a118f4b8a50b9e75e972108a043a8765eec8341a6f", "language": "C/C++", "lines": 253, "truncated": false, "block": 3, "row": 4293 }, { "path": "source/htslib/htslib/ksort.h", "sha256": "bd5fba9d83217ef6af40fc0580247ede47af1f6a436a6cf1b818e41d7b43effa", "language": "C/C++", "lines": 285, "truncated": false, "block": 3, "row": 4332 }, { "path": "source/htslib/htslib/kstdint.h", "sha256": "9c1d2b38b5d4a756ede1608b114cad019d8cd168c0578fe6b0a897f32c7b4d21", "language": "C/C++", "lines": 64, "truncated": false, "block": 3, "row": 3846 }, { "path": "source/htslib/htslib/kstring.h", "sha256": "26025b699925289407f2eb0d8f436aceed28d105bd9b329c4547c0b3aafa3ba4", "language": "C/C++", "lines": 270, "truncated": false, "block": 3, "row": 4183 }, { "path": "source/htslib/htslib/sam.h", "sha256": "edd76b4e9cf78c2d9ad840182e387b91f9dcd6f00ffcf88ee0f59ddfc954391c", "language": "C/C++", "lines": 401, "truncated": false, "block": 3, "row": 4419 }, { "path": "source/htslib/htslib/synced_bcf_reader.h", "sha256": "d0b63c05fd5bc99f7496cb1277acdc7abe48cce26c64f23a9098f79ffda94823", "language": "C/C++", "lines": 255, "truncated": false, "block": 3, "row": 4350 }, { "path": "source/htslib/htslib/tbx.h", "sha256": "16d4d2f250c59f272a1717b849693d6356ebb94dd2c07703c668a4dbec47cc21", "language": "C/C++", "lines": 52, "truncated": false, "block": 3, "row": 3662 }, { "path": "source/htslib/htslib/vcf.h", "sha256": "3486609897d78270a319877af726690f566872e35f8fe3004482e5b499f3c2e6", "language": "C/C++", "lines": 824, "truncated": false, "block": 3, "row": 4592 }, { "path": "source/htslib/htslib/vcf_sweep.h", "sha256": "8fdfdc20c7e8cac51f80cb7b35965bcbd5c95408e899d79a30ee191705938407", "language": "C/C++", "lines": 15, "truncated": false, "block": 3, "row": 3384 }, { "path": "source/htslib/htslib/vcfutils.h", "sha256": "389059e7d0b6d00070fb50c05202672164bb9cdf0fcecfd5b25fa890b0ab76c4", "language": "C/C++", "lines": 94, "truncated": false, "block": 3, "row": 3908 }, { "path": "source/htslib/kfunc.c", "sha256": "b5025ccdfc1ca51e7393c29a323f2b4c6074c612addb46199075d06e9f0a9405", "language": "C", "lines": 254, "truncated": false, "block": 3, "row": 206 }, { "path": "source/htslib/knetfile.c", "sha256": "f7e7248d31751700c4314dc983fd8cb535ce6adad7b20d57903487f13d6b0778", "language": "C", "lines": 622, "truncated": false, "block": 3, "row": 286 }, { "path": "source/htslib/kstring.c", "sha256": "ad779c5886b130f565b0912300f11c7b1db86b0cedf94324fd70e771fef12c7b", "language": "C", "lines": 229, "truncated": false, "block": 3, "row": 156 }, { "path": "source/htslib/sam.c", "sha256": "ec9101874c9a528952759b65136bce1073553e0e66dbf48eac92c32f9a86699f", "language": "C", "lines": 1797, "truncated": false, "block": 3, "row": 324 }, { "path": "source/htslib/synced_bcf_reader.c", "sha256": "24b8bda691d6e39acd258c5545068e04f24be3f89ab2174a0088b758c1b348d3", "language": "C", "lines": 1183, "truncated": false, "block": 3, "row": 316 }, { "path": "source/htslib/tabix.c", "sha256": "22565252fbf98da8282fea5cdd31cff23851ba2182434eb577757d04d9bc4cbb", "language": "C", "lines": 374, "truncated": false, "block": 3, "row": 259 }, { "path": "source/htslib/tbx.c", "sha256": "00bb9fa5203e3c0d89539dcbd5bfcfcbf6a0a9318362c5daf3bf8f7e3b8184a0", "language": "C", "lines": 290, "truncated": false, "block": 3, "row": 202 }, { "path": "source/htslib/vcf.c", "sha256": "d2a3a111f77506f37d6b30226b237e72747cd33bc3b19dc9015bf4b20cff0f73", "language": "C", "lines": 2967, "truncated": false, "block": 3, "row": 338 }, { "path": "source/htslib/vcf_sweep.c", "sha256": "052e2a4e894f59e89e95dd7da8a73e446af68097916083b85e247ec06c5887ba", "language": "C", "lines": 158, "truncated": false, "block": 3, "row": 116 }, { "path": "source/htslib/vcfutils.c", "sha256": "4a1baffc6f61a5dda8855904ea00d2da9ab9f488e25c71e3c3d46e17ce6e8848", "language": "C", "lines": 642, "truncated": false, "block": 3, "row": 296 }, { "path": "source/insertSeqSA.cpp", "sha256": "30ec5822900f49e232ddd86e577cda63dfdbb1cecc61205a0d8dac31239d3273", "language": "C++", "lines": 319, "truncated": false, "block": 3, "row": 3069 }, { "path": "source/insertSeqSA.h", "sha256": "5b5aa11fbe3e0c58356e7097d235af1f82b7d9596473f18d49371861eb418264", "language": "C/C++", "lines": 11, "truncated": false, "block": 3, "row": 3375 }, { "path": "source/mapThreadsSpawn.cpp", "sha256": "b8ce2f8f64b5547ec56906a0cbd93eacebd329f24a23b597712c2de82c8898ef", "language": "C++", "lines": 33, "truncated": false, "block": 3, "row": 1660 }, { "path": "source/mapThreadsSpawn.h", "sha256": "ee3d09d827928d7d30fc4e3a70334a83e4220da8135ff6adc33c1fb6603eb26f", "language": "C/C++", "lines": 7, "truncated": false, "block": 3, "row": 3336 }, { "path": "source/opal/opal.cpp", "sha256": "87abdb0d848bf4466474082080cf6772b332744663197274070838e7d4bc88df", "language": "C++", "lines": 1568, "truncated": false, "block": 3, "row": 3284 }, { "path": "source/opal/opal.h", "sha256": "b13bb1f5367dad6556dae903f4d344bb5f4da05fb608744e170d5ed861c1aa24", "language": "C/C++", "lines": 171, "truncated": false, "block": 3, "row": 4265 }, { "path": "source/opal/simde_avx2.h", "sha256": "7870ed6e4856e8c08bcd9b8aca404783382642468e8dafdce9337baf08ef6761", "language": "C/C++", "lines": 5590, "truncated": true, "block": 3, "row": 4626 }, { "path": "source/outputSJ.cpp", "sha256": "744bc9102efdf4f68cd0a0f44dd28e71871659623d0ff771b9502255c76f262f", "language": "C++", "lines": 163, "truncated": false, "block": 3, "row": 2824 }, { "path": "source/outputSJ.h", "sha256": "06412e22e5166c09c1c2f9639f84f7c930d8246864fe887b488890ec2f82527c", "language": "C/C++", "lines": 4, "truncated": false, "block": 3, "row": 3324 }, { "path": "source/readBarcodeLoad.h", "sha256": "7ca46b463eaf4d32368af3999ede2212729f18a6d3a7c8b85af3892654e47750", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3340 }, { "path": "source/readLoad.cpp", "sha256": "696023e6827042ec507cf2ac4d84443643a50e598fbcc37831e00ae133bc5fc2", "language": "C++", "lines": 100, "truncated": false, "block": 3, "row": 2451 }, { "path": "source/readLoad.h", "sha256": "04ab96f887b47f722f67cd996256c01e9adc64c1e0e712136b5b3a3510ac0bee", "language": "C/C++", "lines": 12, "truncated": false, "block": 3, "row": 3393 }, { "path": "source/samHeaders.cpp", "sha256": "3bfe2cff312f8c48833e6de6de0ca6eb122e5eeea109eb1821a9837efa2e671d", "language": "C++", "lines": 108, "truncated": false, "block": 3, "row": 2367 }, { "path": "source/samHeaders.h", "sha256": "79746c42ee4d62792542e377b6f966621de949c83d276d798fb208a89e7f43e3", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3341 }, { "path": "source/serviceFuns.cpp", "sha256": "ee860d4535b8d04ef3e76e624a7d222823ac93aefede7f45e137377751ff4998", "language": "C++", "lines": 351, "truncated": false, "block": 3, "row": 2839 }, { "path": "source/signalFromBAM.cpp", "sha256": "f0608019ff9447c5f38088642e445baae0f3a7735c19722ec1db756460569861", "language": "C++", "lines": 209, "truncated": false, "block": 3, "row": 2913 }, { "path": "source/signalFromBAM.h", "sha256": "062b890748f731bb8d56cd03c0603d15f9739d97e53d64d79adc80ce3040ce16", "language": "C/C++", "lines": 13, "truncated": false, "block": 3, "row": 3366 }, { "path": "source/sjAlignSplit.cpp", "sha256": "29bb5b3df70f4a8bb9ea72834ed67f3b5284381e25082317718114eda77fc279", "language": "C++", "lines": 15, "truncated": false, "block": 3, "row": 839 }, { "path": "source/sjAlignSplit.h", "sha256": "c28341baa151881592a16efd939130d2d945550c9cb2517af95c66baecb877ac", "language": "C/C++", "lines": 9, "truncated": false, "block": 3, "row": 3349 }, { "path": "source/sjdbBuildIndex.cpp", "sha256": "1e050eba0686aa88c5ea1d992c529215a22c07eae62d8f9d184a602ea4621588", "language": "C++", "lines": 333, "truncated": false, "block": 3, "row": 3099 }, { "path": "source/sjdbBuildIndex.h", "sha256": "066d409e8341c37ce68756269ff911b4aa6c9bd15784b62c91ed0321565d0ce8", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3364 }, { "path": "source/sjdbInsertJunctions.cpp", "sha256": "2bb05df7d1665f86c7ce0667e94fdaa8910c0d806565faece0af4fe54c681e3b", "language": "C++", "lines": 102, "truncated": false, "block": 3, "row": 2700 }, { "path": "source/sjdbInsertJunctions.h", "sha256": "14cdf4d622091e1215d5a56f2568d7833fb184eaacbe74db64bea5282d250338", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3351 }, { "path": "source/sjdbLoadFromFiles.cpp", "sha256": "fbafeee5c81447b968d31caf749e14f5386365c9fd6aca5e7a3a441e7010602c", "language": "C++", "lines": 27, "truncated": false, "block": 3, "row": 1299 }, { "path": "source/sjdbLoadFromFiles.h", "sha256": "da3dc5a92bf76102cd4f8941109e50a753dd59fc8dd53ee47088d6d5b0420cca", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3339 }, { "path": "source/sjdbLoadFromStream.cpp", "sha256": "fce127fc96d34d9e2539b1e05feb85f25a14a40d54365c8f570066c40d00e983", "language": "C++", "lines": 29, "truncated": false, "block": 3, "row": 1099 }, { "path": "source/sjdbLoadFromStream.h", "sha256": "ae582d7638d1798ee746adf421d557e6c4f062ba8e4ae4abc7aae269c6e77ef0", "language": "C/C++", "lines": 8, "truncated": false, "block": 3, "row": 3337 }, { "path": "source/sjdbPrepare.cpp", "sha256": "fe8269c7c9ba47132d9d8d3076589d099b9f9d3cbc749dbf31381140bbbc7b46", "language": "C++", "lines": 225, "truncated": false, "block": 3, "row": 3001 }, { "path": "source/sjdbPrepare.h", "sha256": "d82dbc48e13349a8fa0ebd7f6b950121da8a51979866b94e665e6b189ea9c6e2", "language": "C/C++", "lines": 10, "truncated": false, "block": 3, "row": 3350 }, { "path": "source/soloInputFeatureUMI.cpp", "sha256": "0639397f292cd8e933b6f56eefbbb9dfb8cd3425f6702011cf4aa1884340700b", "language": "C++", "lines": 44, "truncated": false, "block": 3, "row": 1439 }, { "path": "source/soloInputFeatureUMI.h", "sha256": "ac7b18870b2738f50b25185864e7316038dc6ba9d880fca0f4d8f80f81914e7b", "language": "C/C++", "lines": 13, "truncated": false, "block": 3, "row": 3405 }, { "path": "source/sortSuffixesBucket.h", "sha256": "6da1efdc5aacdd913e0aba4fe990c092f5007eca8525bb52cc17c01a8a1e2b20", "language": "C/C++", "lines": 3, "truncated": false, "block": 3, "row": 3323 }, { "path": "source/stitchAlignToTranscript.cpp", "sha256": "84d31fff54c1d5a3b8eda85f0d1abdd49227536b58e371d1e8146f526913fc5d", "language": "C++", "lines": 415, "truncated": false, "block": 3, "row": 3198 }, { "path": "source/stitchAlignToTranscript.h", "sha256": "53b0b59e982b3463e7b74f4f1583b4c30daac250fc1b0fbdf6ebec75ac1a926d", "language": "C/C++", "lines": 7, "truncated": false, "block": 3, "row": 3372 }, { "path": "source/stitchGapIndel.cpp", "sha256": "cffb0ce5535117d44290b25a63aec8b650ec37f66786ddba5e229c0d088c3fba", "language": "C++", "lines": 59, "truncated": false, "block": 3, "row": 1766 }, { "path": "source/stitchWindowAligns.cpp", "sha256": "2e38ad92980341af9bcccf48fb76a3bad6f2934a550f1e453ab9760140a9482e", "language": "C++", "lines": 355, "truncated": false, "block": 3, "row": 3160 }, { "path": "source/stitchWindowAligns.h", "sha256": "f97cce62b7fb4a9e09e7521d83cbc1dc3e74e23cab24c6b251e30da5df55c54d", "language": "C/C++", "lines": 12, "truncated": false, "block": 3, "row": 3418 }, { "path": "source/streamFuns.cpp", "sha256": "3d108260710811b22433dbf1e100b7333c4d057a1ddd002ed7ec9ff1106d41bb", "language": "C++", "lines": 149, "truncated": false, "block": 3, "row": 2794 }, { "path": "source/streamFuns.h", "sha256": "05ded052748f60b0258196d48a754126919936092ea510b351b1c472954236e5", "language": "C/C++", "lines": 17, "truncated": false, "block": 3, "row": 3465 }, { "path": "source/stringSubstituteAll.cpp", "sha256": "8acefbc1f6ee5a0476d89673844918d0cc09ddc3444ae34a29834530acafff2d", "language": "C++", "lines": 10, "truncated": false, "block": 3, "row": 730 }, { "path": "source/stringSubstituteAll.h", "sha256": "13fc9fee26fa88b86648a7f68c2d50852d1815924dc5b7a50f1930568f9b9e16", "language": "C/C++", "lines": 8, "truncated": false, "block": 3, "row": 3335 }, { "path": "source/sysRemoveDir.cpp", "sha256": "7bd3dc835300bb0fd90c86fb18b784c0cfd0b58da848105ee1307bfa0503ca3b", "language": "C++", "lines": 28, "truncated": false, "block": 3, "row": 969 }, { "path": "source/sysRemoveDir.h", "sha256": "068797768ce12c98fa48bd59cd0636eafc2cf64dc84c590f2d3e708054e7c949", "language": "C/C++", "lines": 8, "truncated": false, "block": 3, "row": 3325 }, { "path": "source/systemFunctions.cpp", "sha256": "52b4d42ae489360b6648fb82e99e2ba561a38acf4ebe590af5f159c98525b3da", "language": "C++", "lines": 27, "truncated": false, "block": 3, "row": 889 }, { "path": "source/systemFunctions.h", "sha256": "8c362ee417bed051cd49903d4bb49b6e2214c98e0d068bc610b3da929949bfc5", "language": "C/C++", "lines": 6, "truncated": false, "block": 3, "row": 3321 }, { "path": "source/twoPassRunPass1.cpp", "sha256": "287b18b27ab0a593c51c1afbbc117347f136fff0ca693448c72a4490fa81e6da", "language": "C++", "lines": 97, "truncated": false, "block": 3, "row": 2146 }, { "path": "source/twoPassRunPass1.h", "sha256": "07901af998d59bca5682f65c8c6a34ab852db4ad93d7b461276702bdfac227af", "language": "C/C++", "lines": 11, "truncated": false, "block": 3, "row": 3360 } ] }