OpenScientificCodeRegistry/Database
Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/alexdobin/star",4 "url": "https://github.com/alexdobin/STAR",5 "host": "github.com",6 "commit": "b1edc1208d91a53bf40ebae8669f71d50b994851",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "551e5bc4f91bf85b75c848aabba5acbcff4f4adf75e606cd17787038a155e69f",14 "language": "License",15 "lines": 21,16 "truncated": false,17 "block": 3,18 "row": 802319 },20 {21 "path": "README.md",22 "sha256": "702eb50c9aa3e0ab3a8bcd251eca90ab8dd4cf3833d9bcdf25db218ce669e3e3",23 "language": "Text",24 "lines": 115,25 "truncated": false,26 "block": 4,27 "row": 248628 },29 {30 "path": "extras/scripts/extractSJfromGTF.sh",31 "sha256": "356b312af0e585f87f6596f3771f70e3fdd707024d96feeccaffc72d08522086",32 "language": "Shell",33 "lines": 10,34 "truncated": false,35 "block": 4,36 "row": 139337 },38 {39 "path": "extras/scripts/sjMotif.m",40 "sha256": "4e1ea6d0c0c148099ad2b49b1d2d9e4e7564a94684e92873e9394294f7dd4ce1",41 "language": "MATLAB",42 "lines": 45,43 "truncated": false,44 "block": 3,45 "row": 1015846 },47 {48 "path": "source/AlignVsTranscript.h",49 "sha256": "c3713f7dfff0f2e66c38170cdae17cdc8bad257f55b507f9d113dc1e22ba8148",50 "language": "C/C++",51 "lines": 9,52 "truncated": false,53 "block": 3,54 "row": 333455 },56 {57 "path": "source/BAMbinSortByCoordinate.cpp",58 "sha256": "c6db83dea84586227b9c33455f044a14bc4c071598bcfdb13f9d14ce55d257ff",59 "language": "C++",60 "lines": 81,61 "truncated": false,62 "block": 3,63 "row": 225564 },65 {66 "path": "source/BAMbinSortByCoordinate.h",67 "sha256": "f42323a77e39386c9e93da9818c274e2a8947c318aba19f39f677169a4fedc68",68 "language": "C/C++",69 "lines": 12,70 "truncated": false,71 "block": 3,72 "row": 338273 },74 {75 "path": "source/BAMbinSortUnmapped.cpp",76 "sha256": "ed4bf4e1866f89fb69f3293346da6e6a5eca685f48d7abbfeb091fdcf6476853",77 "language": "C++",78 "lines": 91,79 "truncated": false,80 "block": 3,81 "row": 234582 },83 {84 "path": "source/BAMbinSortUnmapped.h",85 "sha256": "e8be7aa723afb4fc7db0e2eab13b6e50732571457d510092d4b100069cdb5020",86 "language": "C/C++",87 "lines": 12,88 "truncated": false,89 "block": 3,90 "row": 337091 },92 {93 "path": "source/BAMfunctions.cpp",94 "sha256": "ca7faa893c749db90777b2e5c48ddb56bb91c5159483ba22c0cd36b5e295df92",95 "language": "C++",96 "lines": 194,97 "truncated": false,98 "block": 3,99 "row": 2767100 },101 {102 "path": "source/BAMfunctions.h",103 "sha256": "24ae61be831accbec19b46a87e227821b8d704707d0df448025fce0de1e8ca88",104 "language": "C/C++",105 "lines": 79,106 "truncated": false,107 "block": 3,108 "row": 3946109 },110 {111 "path": "source/BAMoutput.cpp",112 "sha256": "12b8e120b181964996f47177195bbe52a25cfdc605fa9614930a6a5cc9e00fcc",113 "language": "C++",114 "lines": 186,115 "truncated": false,116 "block": 3,117 "row": 2791118 },119 {120 "path": "source/BAMoutput.h",121 "sha256": "0fc676c33b0748fcd216a1cf4152946d050e53497777b8c2f6de1c06778572e5",122 "language": "C/C++",123 "lines": 37,124 "truncated": false,125 "block": 3,126 "row": 3571127 },128 {129 "path": "source/Chain.cpp",130 "sha256": "d48d64e7ba78d6d13382e0fdb93ab9641486251e77d56e3bf2cf5c67e8fc98ba",131 "language": "C++",132 "lines": 126,133 "truncated": false,134 "block": 3,135 "row": 2520136 },137 {138 "path": "source/Chain.h",139 "sha256": "d7a2922315abc3ccf4cb5a4fc3ba3366238aad40838da04ce8dec3e9a5f86471",140 "language": "C/C++",141 "lines": 30,142 "truncated": false,143 "block": 3,144 "row": 3440145 },146 {147 "path": "source/ChimericAlign.cpp",148 "sha256": "349be7139d8518b3864a6680e9d01662283dcc6b4d296903c49eb5d504c7650e",149 "language": "C++",150 "lines": 32,151 "truncated": false,152 "block": 3,153 "row": 1492154 },155 {156 "path": "source/ChimericAlign.h",157 "sha256": "b55c719978db9c56d22f4183f61b9c581ae3fe51f9a7c84744e714871923be9c",158 "language": "C/C++",159 "lines": 41,160 "truncated": false,161 "block": 3,162 "row": 3595163 },164 {165 "path": "source/ChimericAlign_chimericBAMoutput.cpp",166 "sha256": "076d74764691a18af95b53b9388a677be9b2b3acfb3ad9edfb06d2ffcf894f9a",167 "language": "C++",168 "lines": 105,169 "truncated": false,170 "block": 3,171 "row": 2599172 },173 {174 "path": "source/ChimericAlign_chimericJunctionOutput.cpp",175 "sha256": "8fe67cefcd859e657f9d1f2881dfe5757cb7aa2c16f871fde19bbc8f581b6649",176 "language": "C++",177 "lines": 23,178 "truncated": false,179 "block": 3,180 "row": 1686181 },182 {183 "path": "source/ChimericAlign_chimericStitching.cpp",184 "sha256": "7e004ab84473afa1d914fce54c4ee7b1a92e7ae6d5058f840d7c19af29978cd4",185 "language": "C++",186 "lines": 181,187 "truncated": false,188 "block": 3,189 "row": 2742190 },191 {192 "path": "source/ChimericDetection.cpp",193 "sha256": "c9182a6284abc57f1b3755af8f4daf55479ca192810442f9c857bffcf797b5bd",194 "language": "C++",195 "lines": 6,196 "truncated": false,197 "block": 3,198 "row": 702199 },200 {201 "path": "source/ChimericDetection.h",202 "sha256": "e25c2390ebd9b48102e51d4cf0f73062cdcd606b7c224e9986610524a0ba4352",203 "language": "C/C++",204 "lines": 29,205 "truncated": false,206 "block": 3,207 "row": 3449208 },209 {210 "path": "source/ChimericDetection_chimericDetectionMult.cpp",211 "sha256": "6c7d9250fbb1b72b38c67ce16d3b4ea1f3f47ced34a8388e30f3daa601729985",212 "language": "C++",213 "lines": 138,214 "truncated": false,215 "block": 3,216 "row": 2728217 },218 {219 "path": "source/ChimericSegment.cpp",220 "sha256": "04626d428b777f80ef6e38a1c4ec1ceaa85039f2916911f7c8b00c3a808cad74",221 "language": "C++",222 "lines": 32,223 "truncated": false,224 "block": 3,225 "row": 1672226 },227 {228 "path": "source/ChimericSegment.h",229 "sha256": "bb086a8ab9621e859469bcf4b04f68ee8ca408e5949cda8f8e2fc7722fc2f6a1",230 "language": "C/C++",231 "lines": 23,232 "truncated": false,233 "block": 3,234 "row": 3420235 },236 {237 "path": "source/ChimericTranscript.h",238 "sha256": "d010357e10b6c898d626af8ea95d3517d623390a3b996176405215c41f8ad0d6",239 "language": "C/C++",240 "lines": 19,241 "truncated": false,242 "block": 3,243 "row": 3412244 },245 {246 "path": "source/ClipCR4.cpp",247 "sha256": "ff398e5cce959ee753e913c9497376151598ea2b788721d722bbab9552cf64a3",248 "language": "C++",249 "lines": 109,250 "truncated": false,251 "block": 3,252 "row": 2070253 },254 {255 "path": "source/ClipCR4.h",256 "sha256": "ac05d9bd4b89046b83732e1ccc1706882f7e0a6a2b34b9857e2cbd42b51446ec",257 "language": "C/C++",258 "lines": 41,259 "truncated": false,260 "block": 3,261 "row": 3458262 },263 {264 "path": "source/ClipMate.h",265 "sha256": "0c9b461e6b4e28931f3f871bc70bec540a68bc3aaa98181673d7a47cfa2dc95b",266 "language": "C/C++",267 "lines": 34,268 "truncated": false,269 "block": 3,270 "row": 3456271 },272 {273 "path": "source/ClipMate_clip.cpp",274 "sha256": "5984fcab7743aebb2e1c3a79c650d61ab7477a6b824ef1b6d8132338f92912ae",275 "language": "C++",276 "lines": 78,277 "truncated": false,278 "block": 3,279 "row": 1919280 },281 {282 "path": "source/ClipMate_clipChunk.cpp",283 "sha256": "f685a456665f8f3f6e6b56b149d11d76c00de9157352b7f60da8b8f3542046b4",284 "language": "C++",285 "lines": 62,286 "truncated": false,287 "block": 3,288 "row": 1742289 },290 {291 "path": "source/ClipMate_initialize.cpp",292 "sha256": "55488425a7f78fd92ea5b366be8f9c0b4c5c533bc68b97163fca8ce7036a7e5e",293 "language": "C++",294 "lines": 32,295 "truncated": false,296 "block": 3,297 "row": 1011298 },299 {300 "path": "source/ErrorWarning.cpp",301 "sha256": "e0931d14f98a1916abb99ec344fb50ffd68bd5a63a49855586a1b41f1d753a18",302 "language": "C++",303 "lines": 37,304 "truncated": false,305 "block": 3,306 "row": 1402307 },308 {309 "path": "source/ErrorWarning.h",310 "sha256": "f2e927b958a4230c6fd85535203e2e711ff4d651c8060add98d58f85a8639671",311 "language": "C/C++",312 "lines": 9,313 "truncated": false,314 "block": 3,315 "row": 3377316 },317 {318 "path": "source/GTF.cpp",319 "sha256": "9254afb2a2fa8ff3e751d9bfafd2b86f4d389ee8b6e647ad09416dd61962229c",320 "language": "C++",321 "lines": 171,322 "truncated": false,323 "block": 3,324 "row": 2888325 },326 {327 "path": "source/GTF.h",328 "sha256": "4fb9ffd8118f9a97762d392cd5dd950dbdad6cd9888f06119febb4116a98224f",329 "language": "C/C++",330 "lines": 36,331 "truncated": false,332 "block": 3,333 "row": 3475334 },335 {336 "path": "source/GTF_superTranscript.cpp",337 "sha256": "6553a3ebeda538df7327b91730c7d63b3477aecdd77d4e0f95c9d1b87a673f29",338 "language": "C++",339 "lines": 257,340 "truncated": false,341 "block": 3,342 "row": 3064343 },344 {345 "path": "source/GTF_transcriptGeneSJ.cpp",346 "sha256": "dccd988d45418def20a8086fadb7b57a15b9a703e1ccc3586dc3642286c2c297",347 "language": "C++",348 "lines": 183,349 "truncated": false,350 "block": 3,351 "row": 2918352 },353 {354 "path": "source/Genome.cpp",355 "sha256": "ee10043fa3c0053ad4e587fa5ffe2c6baf51e552613ce0a60182c84f1dac0126",356 "language": "C++",357 "lines": 234,358 "truncated": false,359 "block": 3,360 "row": 2990361 },362 {363 "path": "source/Genome.h",364 "sha256": "9483ed26c8739a4c04cc85856257bb0142a6c66a95666e1b3e5333f3b5ee5112",365 "language": "C/C++",366 "lines": 107,367 "truncated": false,368 "block": 3,369 "row": 4023370 },371 {372 "path": "source/Genome_genomeGenerate.cpp",373 "sha256": "3d8fe6cf3685e25cc76c3dcfba12ed68ff2b5946bab22ddedc7996a077ba2124",374 "language": "C++",375 "lines": 438,376 "truncated": false,377 "block": 3,378 "row": 3176379 },380 {381 "path": "source/Genome_genomeLoad.cpp",382 "sha256": "f6a85ef14d13e814d3291ee86ce17599590fb778f65268bbe2eafdf37bc77542",383 "language": "C++",384 "lines": 521,385 "truncated": false,386 "block": 3,387 "row": 3214388 },389 {390 "path": "source/Genome_genomeOutLoad.cpp",391 "sha256": "51d51a2a4f665b6ee6d9158cc9cc07fc21ef2ed075c67e87912909eedf6410d9",392 "language": "C++",393 "lines": 58,394 "truncated": false,395 "block": 3,396 "row": 1851397 },398 {399 "path": "source/Genome_insertSequences.cpp",400 "sha256": "8a72b76d09291d81ca49fcc395ff193803bc4d6144c107e35e5a6a175ea08c7a",401 "language": "C++",402 "lines": 33,403 "truncated": false,404 "block": 3,405 "row": 1386406 },407 {408 "path": "source/Genome_transformGenome.cpp",409 "sha256": "3b0807d1543e0a10cda68cfff9d19849e157048d4976191cd1e44b7efa96c12e",410 "language": "C++",411 "lines": 324,412 "truncated": false,413 "block": 3,414 "row": 3087415 },416 {417 "path": "source/GlobalVariables.cpp",418 "sha256": "f4ccc14a0adadc10b2a124adde5244813c611bcc88210d2ed544c08e06fd6020",419 "language": "C++",420 "lines": 4,421 "truncated": false,422 "block": 3,423 "row": 452424 },425 {426 "path": "source/GlobalVariables.h",427 "sha256": "15f402cde661a5cc115382d805f4c07e41640dfea1e54b8f692c97acae8e9ae9",428 "language": "C/C++",429 "lines": 9,430 "truncated": false,431 "block": 3,432 "row": 3328433 },434 {435 "path": "source/InOutStreams.cpp",436 "sha256": "14d75d256e0ce9e350bdeff6d9d7162cd44626f7e3cbd116a060c270a149b453",437 "language": "C++",438 "lines": 44,439 "truncated": false,440 "block": 3,441 "row": 1187442 },443 {444 "path": "source/InOutStreams.h",445 "sha256": "a152688ffce13341f3ef96901a21537c065d2d79de0e20b588ae0d670687eede",446 "language": "C/C++",447 "lines": 23,448 "truncated": false,449 "block": 3,450 "row": 3419451 },452 {453 "path": "source/IncludeDefine.h",454 "sha256": "0a55688ea42ca47041f2e53011f311300be7891ac3b10bd9de7767bed62af956",455 "language": "C/C++",456 "lines": 255,457 "truncated": false,458 "block": 3,459 "row": 4133460 },461 {462 "path": "source/OutSJ.cpp",463 "sha256": "1e0383cf8ec87833993796388329b7697af2043eca5324034c60b3efd2f8c6ff",464 "language": "C++",465 "lines": 123,466 "truncated": false,467 "block": 3,468 "row": 2513469 },470 {471 "path": "source/OutSJ.h",472 "sha256": "c60630a0024845aef8cc778e18684e77195f90bc7ecc9c7918ce28c21b211099",473 "language": "C/C++",474 "lines": 59,475 "truncated": false,476 "block": 3,477 "row": 3695478 },479 {480 "path": "source/PackedArray.cpp",481 "sha256": "f1aeb9cfa77754d75bfd69b3a0816bd1318a4088c480a5934520f9f85aaf2586",482 "language": "C++",483 "lines": 43,484 "truncated": false,485 "block": 3,486 "row": 1239487 },488 {489 "path": "source/PackedArray.h",490 "sha256": "f876319310d0f3eb405dbd6dbc5c8e7793f360f07497dd46e52e80c7ce5ab77d",491 "language": "C/C++",492 "lines": 34,493 "truncated": false,494 "block": 3,495 "row": 3453496 },497 {498 "path": "source/ParameterInfo.h",499 "sha256": "be3bcaf9d18188bf3e29eda47dba2d644f2af43b343bdab5651e2d6d85f15670",500 "language": "C/C++",501 "lines": 112,502 "truncated": false,503 "block": 3,504 "row": 3943505 },506 {507 "path": "source/Parameters.cpp",508 "sha256": "f303bd6fb1d541924d9f501ffc5266b49f6bda48dfbf593b5ad0d139abd72ae1",509 "language": "C++",510 "lines": 1269,511 "truncated": false,512 "block": 3,513 "row": 3286514 },515 {516 "path": "source/Parameters.h",517 "sha256": "0bb9b86c1159f5fe1f12c241fc5ca3dc7d7a36f67f5bc26cc4fbd9dfbd723387",518 "language": "C/C++",519 "lines": 374,520 "truncated": false,521 "block": 3,522 "row": 4385523 },524 {525 "path": "source/ParametersChimeric.h",526 "sha256": "cd09b75ad62d3e892ecb314f746ec4c19b0706e9fd615f7d69bfc77f097a540b",527 "language": "C/C++",528 "lines": 41,529 "truncated": false,530 "block": 3,531 "row": 3485532 },533 {534 "path": "source/ParametersChimeric_initialize.cpp",535 "sha256": "12d46f39ff22e1a1cc9d5ee169946b1bf433827494b9aef8edfaf36451d07c60",536 "language": "C++",537 "lines": 118,538 "truncated": false,539 "block": 3,540 "row": 2579541 },542 {543 "path": "source/ParametersClip.h",544 "sha256": "4de79db0d8cda758a3cbbf7b8f9527297e55deb79d623565a0e5c521c5b21685",545 "language": "C/C++",546 "lines": 37,547 "truncated": false,548 "block": 3,549 "row": 3430550 },551 {552 "path": "source/ParametersClip_initialize.cpp",553 "sha256": "ca59ff54a49da94444d41d4595f6fd33bb6433ca1613803c5f021a345d90c8e1",554 "language": "C++",555 "lines": 107,556 "truncated": false,557 "block": 3,558 "row": 2609559 },560 {561 "path": "source/ParametersGenome.cpp",562 "sha256": "f7ae6d62627b976614c6e804846d9b3c7a89a442f8d73a5e591fee1a67194706",563 "language": "C++",564 "lines": 59,565 "truncated": false,566 "block": 3,567 "row": 2052568 },569 {570 "path": "source/ParametersGenome.h",571 "sha256": "95c0de173c2a9e4a23002f456b060f349baf2f3a251fd659aa287a6393171ee0",572 "language": "C/C++",573 "lines": 63,574 "truncated": false,575 "block": 3,576 "row": 3671577 },578 {579 "path": "source/ParametersSolo.cpp",580 "sha256": "a08f59600248dbc22a593ecf19ddab5429f6432d7da5d2b7750896d3390ef1c4",581 "language": "C++",582 "lines": 721,583 "truncated": false,584 "block": 3,585 "row": 3255586 },587 {588 "path": "source/ParametersSolo.h",589 "sha256": "46558240ef417718dfbd9c2acc921ceacea9fcad9a36634ac1238794a25c53ba",590 "language": "C/C++",591 "lines": 220,592 "truncated": false,593 "block": 3,594 "row": 4200595 },596 {597 "path": "source/Parameters_closeReadsFiles.cpp",598 "sha256": "9c476fdb88bf3c370eb9445c1c19632cac18a1dcce53a87ebc7b79357f10945d",599 "language": "C++",600 "lines": 12,601 "truncated": false,602 "block": 3,603 "row": 716604 },605 {606 "path": "source/Parameters_openReadsFiles.cpp",607 "sha256": "9a868132fa48a3b9dda5e79a802abd8d6c80430b27c33e1531d26fcb1a7823cc",608 "language": "C++",609 "lines": 111,610 "truncated": false,611 "block": 3,612 "row": 2552613 },614 {615 "path": "source/Parameters_readFilesInit.cpp",616 "sha256": "d9672c1b51c578a3c2f781917c06a5820a27ffb5df498509562a4544e8c37c46",617 "language": "C++",618 "lines": 167,619 "truncated": false,620 "block": 3,621 "row": 2935622 },623 {624 "path": "source/Parameters_readSAMheader.cpp",625 "sha256": "36cb976f306358464e7b3a30099e29868656482143d2203b8f6775c9fed34eb4",626 "language": "C++",627 "lines": 44,628 "truncated": false,629 "block": 3,630 "row": 1699631 },632 {633 "path": "source/Parameters_samAttributes.cpp",634 "sha256": "8d5f074755e0e5aacaa763d079020102a178f16d3bf78f2fa9cf347b040e6b9e",635 "language": "C++",636 "lines": 263,637 "truncated": false,638 "block": 3,639 "row": 3063640 },641 {642 "path": "source/Quantifications.cpp",643 "sha256": "84563f355c50ba7b87f23812d905927ebec27f9c8d7714dd848114b7c116c88c",644 "language": "C++",645 "lines": 37,646 "truncated": false,647 "block": 3,648 "row": 1250649 },650 {651 "path": "source/Quantifications.h",652 "sha256": "7d315502780691220bf3b9e86d544caeddd56a3ef0edf82072e144197f3faba6",653 "language": "C/C++",654 "lines": 22,655 "truncated": false,656 "block": 3,657 "row": 3436658 },659 {660 "path": "source/ReadAlign.cpp",661 "sha256": "c222d7f923c57652abf3fa4cf734a86ffacd5453ccdb4fbfbcca9852d40c5b15",662 "language": "C++",663 "lines": 125,664 "truncated": false,665 "block": 3,666 "row": 2458667 },668 {669 "path": "source/ReadAlign.h",670 "sha256": "a5edf0b7b9b880eec6ea1f610fbb8c07716a855649c36c36dd0327df8534f3c4",671 "language": "C/C++",672 "lines": 239,673 "truncated": false,674 "block": 3,675 "row": 4309676 },677 {678 "path": "source/ReadAlignChunk.cpp",679 "sha256": "bce6c5cd11d3b3ddac00f21e3058945c0139c678bdf0b453ce24d55de2677537",680 "language": "C++",681 "lines": 170,682 "truncated": false,683 "block": 3,684 "row": 2690685 },686 {687 "path": "source/ReadAlignChunk.h",688 "sha256": "8a8ec5563637e49d752f1725432fd556caba4083e1fd4bbb2f0566f457550eb5",689 "language": "C/C++",690 "lines": 49,691 "truncated": false,692 "block": 3,693 "row": 3681694 },695 {696 "path": "source/ReadAlignChunk_mapChunk.cpp",697 "sha256": "e27e8ec505f05f073e16e606a04e0817e6432c60e94d04d4d3c30e6a09613b84",698 "language": "C++",699 "lines": 128,700 "truncated": false,701 "block": 3,702 "row": 2772703 },704 {705 "path": "source/ReadAlignChunk_processChunks.cpp",706 "sha256": "250c1c61a2fb9be783e5627cb4b4d776e264d754cde2cf869e46d0a579744a3a",707 "language": "C++",708 "lines": 302,709 "truncated": false,710 "block": 3,711 "row": 3171712 },713 {714 "path": "source/ReadAlign_CIGAR.cpp",715 "sha256": "d5bd49fb93f637bd36826f9ff4da1b88e63142f6ff25ac21dff2fe55416c821e",716 "language": "C++",717 "lines": 62,718 "truncated": false,719 "block": 3,720 "row": 2045721 },722 {723 "path": "source/ReadAlign_alignBAM.cpp",724 "sha256": "164bc33ddca4d8cb5057d33b1050a4b1ee6af9eb62359308e296feea9d8cdfe8",725 "language": "C++",726 "lines": 614,727 "truncated": false,728 "block": 3,729 "row": 3236730 },731 {732 "path": "source/ReadAlign_assignAlignToWindow.cpp",733 "sha256": "96a6a1ca0fa56b63e5eeb0d1f38311b52d748c0021c386aded65e087f51b1f07",734 "language": "C++",735 "lines": 130,736 "truncated": false,737 "block": 3,738 "row": 2568739 },740 {741 "path": "source/ReadAlign_calcCIGAR.cpp",742 "sha256": "3e92b38834419af1c610d8907a0624e6301ed9c83afe22ef41ff3871502d899a",743 "language": "C++",744 "lines": 58,745 "truncated": false,746 "block": 3,747 "row": 1889748 },749 {750 "path": "source/ReadAlign_chimericDetection.cpp",751 "sha256": "e83d7e5dd81150d123adeb09f7ad78839e5f2cdf9897e433faeeb4b4f3169238",752 "language": "C++",753 "lines": 57,754 "truncated": false,755 "block": 3,756 "row": 1741757 },758 {759 "path": "source/ReadAlign_chimericDetectionOld.cpp",760 "sha256": "0aaf72c4c884633df0f4059fba250799fdbd3f2f174f9c9b53bf845c159308bd",761 "language": "C++",762 "lines": 312,763 "truncated": false,764 "block": 3,765 "row": 3120766 },767 {768 "path": "source/ReadAlign_chimericDetectionOldOutput.cpp",769 "sha256": "02f91d3ed125fe6e9fa893b148e7cf71ecc33190e77b03d2144630c537767113",770 "language": "C++",771 "lines": 74,772 "truncated": false,773 "block": 3,774 "row": 2289775 },776 {777 "path": "source/ReadAlign_chimericDetectionPEmerged.cpp",778 "sha256": "edb0549cffa248837a61fc68611b6a2755b6edd60c4edad9e1276ebbc1e89af2",779 "language": "C++",780 "lines": 39,781 "truncated": false,782 "block": 3,783 "row": 1215784 },785 {786 "path": "source/ReadAlign_createExtendWindowsWithAlign.cpp",787 "sha256": "1e8e3813a066390427e12defc13004e5b678663ab16c048d097b9056b84a942d",788 "language": "C++",789 "lines": 85,790 "truncated": false,791 "block": 3,792 "row": 2271793 },794 {795 "path": "source/ReadAlign_mapOneRead.cpp",796 "sha256": "28fccbe8df679125525a783b8e84352d5e4e3edc73fa33bc0c352a07683775aa",797 "language": "C++",798 "lines": 118,799 "truncated": false,800 "block": 3,801 "row": 2560802 },803 {804 "path": "source/ReadAlign_mapOneReadSpliceGraph.cpp",805 "sha256": "228b0e5a64b44772f5ea62ebefcdbe7379211fc8ea0fbd2cc5f120379edcd5d5",806 "language": "C++",807 "lines": 40,808 "truncated": false,809 "block": 3,810 "row": 1278811 },812 {813 "path": "source/ReadAlign_mappedFilter.cpp",814 "sha256": "27e695f0b752d5e36871a1f72a081c1420f749c1a4c05e282d907e7f8ccafaf9",815 "language": "C++",816 "lines": 21,817 "truncated": false,818 "block": 3,819 "row": 1103820 },821 {822 "path": "source/ReadAlign_maxMappableLength2strands.cpp",823 "sha256": "cdff4d368b127cab3e9e3cdb3c09708940472d12f3c43fa271dbeb048f3ba6b6",824 "language": "C++",825 "lines": 115,826 "truncated": false,827 "block": 3,828 "row": 2497829 },830 {831 "path": "source/ReadAlign_multMapSelect.cpp",832 "sha256": "d4379f1b91b4100649599e256e587ca3639da88ae96cc86aa2045b45b029e9b0",833 "language": "C++",834 "lines": 95,835 "truncated": false,836 "block": 3,837 "row": 2336838 },839 {840 "path": "source/ReadAlign_oneRead.cpp",841 "sha256": "76aa9321c3cf63cc45acd8c16d0b841faec1b9b0aac3e78bbdea865867da9538",842 "language": "C++",843 "lines": 124,844 "truncated": false,845 "block": 3,846 "row": 2439847 },848 {849 "path": "source/ReadAlign_outputAlignments.cpp",850 "sha256": "fa85b7106b2aa29d1de9d9d899078f701b8c18dbeb53456b8e8f1eb663e566c7",851 "language": "C++",852 "lines": 325,853 "truncated": false,854 "block": 3,855 "row": 3161856 },857 {858 "path": "source/ReadAlign_outputSpliceGraphSAM.cpp",859 "sha256": "c0e9eec6a92039b9db44c46b8e5d6158fb4a2070e0a5788893d4ec6f8d273981",860 "language": "C++",861 "lines": 164,862 "truncated": false,863 "block": 3,864 "row": 2638865 },866 {867 "path": "source/ReadAlign_outputTranscriptCIGARp.cpp",868 "sha256": "c3316d152ebac5993a544457f27945fb1f9e194f091c53360c703f2ca3f69f6a",869 "language": "C++",870 "lines": 65,871 "truncated": false,872 "block": 3,873 "row": 2056874 },875 {876 "path": "source/ReadAlign_outputTranscriptSAM.cpp",877 "sha256": "b11673285edd158300b32ee77b20cea9890dcb4665a5c42e615113c4c35ae313",878 "language": "C++",879 "lines": 359,880 "truncated": false,881 "block": 3,882 "row": 3130883 },884 {885 "path": "source/ReadAlign_outputTranscriptSJ.cpp",886 "sha256": "57a815139cf4a0bb6912ea55a6527bebac6066729eaf345f24f1da78e95291de",887 "language": "C++",888 "lines": 56,889 "truncated": false,890 "block": 3,891 "row": 2191892 },893 {894 "path": "source/ReadAlign_outputVariation.cpp",895 "sha256": "fbebdef6f29f00e051babc9956af5cc0dc40582949d04b50c5b45950a40867fb",896 "language": "C++",897 "lines": 13,898 "truncated": false,899 "block": 3,900 "row": 479901 },902 {903 "path": "source/ReadAlign_peOverlapMergeMap.cpp",904 "sha256": "c46fe04e47192bc2792565830378a130b0a412539c8b1d204cb7355286a74fd3",905 "language": "C++",906 "lines": 368,907 "truncated": false,908 "block": 3,909 "row": 3095910 },911 {912 "path": "source/ReadAlign_quantTranscriptome.cpp",913 "sha256": "4b0816764956fb56db48d153c0f2c7176dd5aaec70ceb288fe950ea83570be65",914 "language": "C++",915 "lines": 91,916 "truncated": false,917 "block": 3,918 "row": 2425919 },920 {921 "path": "source/ReadAlign_stitchPieces.cpp",922 "sha256": "c34b9fb0705be6ed2517c921e2513e508cc5b29d7f180d9f0c3534034e8de307",923 "language": "C++",924 "lines": 350,925 "truncated": false,926 "block": 3,927 "row": 3117928 },929 {930 "path": "source/ReadAlign_stitchWindowSeeds.cpp",931 "sha256": "8cb44befc6b019ff71d91bded33db91e48229fe43e410e44dc7bc17f35d3d684",932 "language": "C++",933 "lines": 278,934 "truncated": false,935 "block": 3,936 "row": 3074937 },938 {939 "path": "source/ReadAlign_storeAligns.cpp",940 "sha256": "6352dc72a86d2a07578caf5b7710052b6274366479b53671e810d9a33398a6d1",941 "language": "C++",942 "lines": 160,943 "truncated": false,944 "block": 3,945 "row": 2641946 },947 {948 "path": "source/ReadAlign_transformGenome.cpp",949 "sha256": "e4b1a6007565ece2bb132a79473d935ef05d679aa8eed5f9521b63a8625c0c0a",950 "language": "C++",951 "lines": 74,952 "truncated": false,953 "block": 3,954 "row": 2128955 },956 {957 "path": "source/ReadAlign_waspMap.cpp",958 "sha256": "506f94281348ebabaeb257e45746c0003dabd3273a5b0141164bf363b86dfbca",959 "language": "C++",960 "lines": 128,961 "truncated": false,962 "block": 3,963 "row": 2353964 },965 {966 "path": "source/ReadAnnotations.h",967 "sha256": "86000759f930d4ae0a2b1ab1f87643398280f8ff1361b1bffef1d7d941a08603",968 "language": "C/C++",969 "lines": 47,970 "truncated": false,971 "block": 3,972 "row": 3714973 },974 {975 "path": "source/STAR.cpp",976 "sha256": "e78db2798a32c3f275c1cca717579977224e25c9e0dadba9541f3d038b8683e6",977 "language": "C++",978 "lines": 313,979 "truncated": false,980 "block": 3,981 "row": 3039982 },983 {984 "path": "source/SequenceFuns.cpp",985 "sha256": "9b0dcb17490feea51e96bbe9eac99943fda40fe04d703e1ac81343a46b59e143",986 "language": "C++",987 "lines": 445,988 "truncated": false,989 "block": 3,990 "row": 3126991 },992 {993 "path": "source/SequenceFuns.h",994 "sha256": "66f975beb0e6c9d72ca57a2957fe3601e691859e097cae91188d6932a07ec677",995 "language": "C/C++",996 "lines": 32,997 "truncated": false,998 "block": 3,999 "row": 36861000 },1001 {1002 "path": "source/SharedMemory.cpp",1003 "sha256": "9d769797c1bd81edca8afbd6c884b1ce359017541141c243b2eab97cdc5de6eb",1004 "language": "C++",1005 "lines": 291,1006 "truncated": false,1007 "block": 3,1008 "row": 27351009 },1010 {1011 "path": "source/SharedMemory.h",1012 "sha256": "002d83da1cfb11bb859fcdb8306b1fb9f2c71359db8ffbad14e250de3fc3c5d8",1013 "language": "C/C++",1014 "lines": 182,1015 "truncated": false,1016 "block": 3,1017 "row": 39741018 },1019 {1020 "path": "source/SimpleGoodTuring/sgt.h",1021 "sha256": "2edda77c55ba4373fcce908ff0d53ad952a0ed7620d479371baa2db5edc73eee",1022 "language": "C/C++",1023 "lines": 300,1024 "truncated": false,1025 "block": 3,1026 "row": 43531027 },1028 {1029 "path": "source/SjdbClass.h",1030 "sha256": "7b7f188a241c8beeeb804e4ea44c722f966a9117cc24538ae5bf9c2a19ce98a6",1031 "language": "C/C++",1032 "lines": 17,1033 "truncated": false,1034 "block": 3,1035 "row": 33581036 },1037 {1038 "path": "source/Solo.cpp",1039 "sha256": "33f059b629c62b91d06f7c365e9cf7f9be917e6e08064b933b40fa171a430939",1040 "language": "C++",1041 "lines": 91,1042 "truncated": false,1043 "block": 3,1044 "row": 21831045 },1046 {1047 "path": "source/Solo.h",1048 "sha256": "311e77d3f576e63fe335ff1a200bd750e523c0ec86a0a97803a0aec9377b6e7d",1049 "language": "C/C++",1050 "lines": 30,1051 "truncated": false,1052 "block": 3,1053 "row": 34231054 },1055 {1056 "path": "source/SoloBarcode.cpp",1057 "sha256": "da84f5a70b9ae7665de854554dee7ddbf11889862d122acd25d6fe374c7cd667",1058 "language": "C++",1059 "lines": 152,1060 "truncated": false,1061 "block": 3,1062 "row": 27221063 },1064 {1065 "path": "source/SoloBarcode.h",1066 "sha256": "90fb66c769d23e8d4b66c581f7f5805f06574526171f465565141895ca4cdb25",1067 "language": "C/C++",1068 "lines": 38,1069 "truncated": false,1070 "block": 3,1071 "row": 35961072 },1073 {1074 "path": "source/SoloBarcode_extractBarcode.cpp",1075 "sha256": "a0553205134146a0081f4aaf1510a492ad21d012d60d74ae60cc5ed13563e137",1076 "language": "C++",1077 "lines": 34,1078 "truncated": false,1079 "block": 3,1080 "row": 12571081 },1082 {1083 "path": "source/SoloCommon.h",1084 "sha256": "93868869b5e66d8ab94e7aba97e2e5adcc01d09786025d1590e254e144405a6b",1085 "language": "C/C++",1086 "lines": 80,1087 "truncated": false,1088 "block": 3,1089 "row": 38241090 },1091 {1092 "path": "source/SoloFeature.cpp",1093 "sha256": "f3a7443a1fdb849d652048fba0e01b1f1bab634575874a9b427d3836083ac883",1094 "language": "C++",1095 "lines": 65,1096 "truncated": false,1097 "block": 3,1098 "row": 18591099 },1100 {1101 "path": "source/SoloFeature.h",1102 "sha256": "4185cb5055d5519c87cf5a68a7f65acc73ae3fa25d31dc428148f645ff4134c7",1103 "language": "C/C++",1104 "lines": 110,1105 "truncated": false,1106 "block": 3,1107 "row": 40221108 },1109 {1110 "path": "source/SoloFeatureTypes.h",1111 "sha256": "5f7d2bb2ea1eec942115271fa6ea5479740fecd2877672593aa9cbe739dd4efe",1112 "language": "C/C++",1113 "lines": 12,1114 "truncated": false,1115 "block": 3,1116 "row": 34341117 },1118 {1119 "path": "source/SoloFeature_addBAMtags.cpp",1120 "sha256": "a82e844594127424fdf29a20936906132e12e4624966784f998cca1746e81e12",1121 "language": "C++",1122 "lines": 26,1123 "truncated": false,1124 "block": 3,1125 "row": 10391126 },1127 {1128 "path": "source/SoloFeature_cellFiltering.cpp",1129 "sha256": "5134339f861572cee4c329004169babe803cda181fa2dad60f7c59be5b10a034",1130 "language": "C++",1131 "lines": 131,1132 "truncated": false,1133 "block": 3,1134 "row": 26481135 },1136 {1137 "path": "source/SoloFeature_collapseUMI_Graph.cpp",1138 "sha256": "b35965f41bd65fb8124876a595fb0a50277014ad11d65f035ad115477d7b3aac",1139 "language": "C++",1140 "lines": 172,1141 "truncated": false,1142 "block": 3,1143 "row": 27931144 },1145 {1146 "path": "source/SoloFeature_collapseUMIall.cpp",1147 "sha256": "d2cfbafa3bc933b55b3b2cb55860811c65a0b9863e2290958aae920bda6be295",1148 "language": "C++",1149 "lines": 658,1150 "truncated": false,1151 "block": 3,1152 "row": 32381153 },1154 {1155 "path": "source/SoloFeature_countCBgeneUMI.cpp",1156 "sha256": "ae124ffba531e2bcc56d5a9386916aed5a4b43ab29ec9a813936449bcc8dbacf",1157 "language": "C++",1158 "lines": 112,1159 "truncated": false,1160 "block": 3,1161 "row": 24711162 },1163 {1164 "path": "source/SoloFeature_countSmartSeq.cpp",1165 "sha256": "a23b5dbb34dd35cfc793831be1131fb4a43efba5d7db8821f05fe53a590cd383",1166 "language": "C++",1167 "lines": 159,1168 "truncated": false,1169 "block": 3,1170 "row": 27011171 },1172 {1173 "path": "source/SoloFeature_countVelocyto.cpp",1174 "sha256": "d99af8573a5f4d2eed3b1591dda48a426f021c2164335bc05ee0137c5a7c82f5",1175 "language": "C++",1176 "lines": 166,1177 "truncated": false,1178 "block": 3,1179 "row": 28231180 },1181 {1182 "path": "source/SoloFeature_emptyDrops_CR.cpp",1183 "sha256": "4dbbefadc28ff21cee5f6ab3c656d3001bfbf75c0585b140ed297fa73275570c",1184 "language": "C++",1185 "lines": 231,1186 "truncated": false,1187 "block": 3,1188 "row": 30161189 },1190 {1191 "path": "source/SoloFeature_loadRawMatrix.cpp",1192 "sha256": "d736d66ccb848f086e3b731b003538095345b1b2778627026efe7a86dc0c5d90",1193 "language": "C++",1194 "lines": 141,1195 "truncated": false,1196 "block": 3,1197 "row": 26731198 },1199 {1200 "path": "source/SoloFeature_outputResults.cpp",