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Name Date Size #Lines LOC

..08-Mar-2021-

cigarDel.samH A D08-Mar-2021735 2928

cigarDelHard.samH A D08-Mar-20211 KiB3231

cigarHard.samH A D08-Mar-2021902 3130

cigarIns.samH A D08-Mar-2021609 2827

cigarNonM.samH A D08-Mar-20211.3 KiB3433

cigarPad.samH A D08-Mar-2021609 2827

cigarSkip.samH A D08-Mar-2021609 2827

cigarSoft.samH A D08-Mar-20211.1 KiB3332

clipSam.samH A D08-Mar-20211.3 KiB3837

clipSam3.samH A D08-Mar-20211.3 KiB3837

clipSamL1R2.samH A D08-Mar-20211.3 KiB3837

clipSamL1R2is.samH A D08-Mar-20211.3 KiB3837

convertBam.samH A D08-Mar-20211.3 KiB3837

convertShift.samH A D08-Mar-2021964 3130

diffAshg.samH A D08-Mar-2021714 2524

diffAshg_only1_testDiff3.samH A D08-Mar-2021602 2524

diffAshg_only2_testDiff4.samH A D08-Mar-2021602 2524

diffNoThresh2_only1_testDiff2.samH A D08-Mar-20211 KiB3332

diffNoThresh2_only2_testDiff1.samH A D08-Mar-2021743 2928

diffNoThreshAll.samH A D08-Mar-20211.7 KiB3332

diffNoThreshAll_only1_testDiff1.samH A D08-Mar-2021743 2928

diffNoThreshAll_only2_testDiff2.samH A D08-Mar-20211 KiB3332

diffOrderSam.samH A D08-Mar-2021753 2928

diffOrderSam2.samH A D08-Mar-2021812 2928

diffOrderSam2_only1_testDiff2.samH A D08-Mar-2021891 3231

diffOrderSamPool2.samH A D08-Mar-2021753 2928

diffOrderSamPool2_only1_testDiff1.samH A D08-Mar-2021743 2928

diffOrderSamPool2_only2_testDiff2.samH A D08-Mar-20211 KiB3332

diffOrderSamPool3.samH A D08-Mar-2021753 2928

diffOrderSamPool3_only2_testDiff2.samH A D08-Mar-2021891 3231

diffOrderSamPool4.samH A D08-Mar-2021753 2928

diffOrderSamPool4_only2_testDiff2.samH A D08-Mar-2021891 3231

filter.samH A D08-Mar-20212.4 KiB2423

mergeBamReg1.samH A D08-Mar-20211.2 KiB3635

mergeBamReg13.samH A D08-Mar-20211.3 KiB3837

mergeBamReg1P.samH A D08-Mar-2021909 3130

mergeBamReg1P3.samH A D08-Mar-20211.1 KiB3433

mergeErr1.errH A D08-Mar-2021107 52

mergeErr2.errH A D08-Mar-2021105 52

mergeSam.samH A D08-Mar-20211.7 KiB4645

mergeSam1.samH A D08-Mar-20211.6 KiB3231

mergeSam2.samH A D08-Mar-20211.6 KiB3231

mergeSam3.samH A D08-Mar-20211.5 KiB3029

mergeSamPI1.samH A D08-Mar-20211.5 KiB3029

polishSam.samH A D08-Mar-20211.4 KiB2322

polishSam2.samH A D08-Mar-20211.5 KiB2524

regionNeg1.samH A D08-Mar-2021713 3029

regionRead.samH A D08-Mar-2021756 3029

regionRead2.samH A D08-Mar-2021699 2928

regionRead8.samH A D08-Mar-2021809 3130

regionRead9.samH A D08-Mar-2021897 3231

regionReadNone.samH A D08-Mar-2021609 2827

regionReadRnFile2.samH A D08-Mar-2021981 3332

regionShift.samH A D08-Mar-2021964 3130

revertBam.samH A D08-Mar-20211.4 KiB3837

revertCigarBam.samH A D08-Mar-20211.4 KiB3837

revertCigarSam.samH A D08-Mar-20211.4 KiB3837

revertKeepTagsBam.samH A D08-Mar-20211.5 KiB3837

revertKeepTagsSam.samH A D08-Mar-20211.5 KiB3837

revertQualBam.samH A D08-Mar-20211.4 KiB3837

revertQualSam.samH A D08-Mar-20211.4 KiB3837

revertRmBQBam.samH A D08-Mar-20211.3 KiB3837

revertRmBQSam.samH A D08-Mar-20211.3 KiB3837

revertRmTagsBam.samH A D08-Mar-20211.3 KiB3837

revertRmTagsSam.samH A D08-Mar-20211.3 KiB3837

revertSam.samH A D08-Mar-20211.4 KiB3837

seqBases.samH A D08-Mar-20212.5 KiB2423

seqEquals.samH A D08-Mar-20212.5 KiB2423

seqOrig.samH A D08-Mar-20212.5 KiB2423

splitSortedBam1.samH A D08-Mar-2021964 3332

splitSortedBam2.samH A D08-Mar-2021764 3029

splitSortedBam3.samH A D08-Mar-2021674 2928

splitSortedBamUnknownChrom.samH A D08-Mar-2021713 3029

squeeze.samH A D08-Mar-20211.3 KiB3837

squeezeBam.samH A D08-Mar-20211.3 KiB3837

squeezeBinQual.samH A D08-Mar-20211.3 KiB3837

squeezeBinQualHigh.samH A D08-Mar-20211.3 KiB3837

squeezeBinQualMid.samH A D08-Mar-20211.3 KiB3837

squeezeKeep.samH A D08-Mar-20211.6 KiB4140

squeezeReadName.samH A D08-Mar-20211.1 KiB3837

squeezeReadNameSorted.samH A D08-Mar-20211.1 KiB3837

squeezeReadNameUnsorted.samH A D08-Mar-20211.1 KiB3837

squeezeTags.samH A D08-Mar-20211.2 KiB3837

testBam2FastQCoord.fastqH A D08-Mar-2021390 2928

testBam2FastQCoordAll1.fastqH A D08-Mar-20212.6 KiB189188

testBam2FastQCoordChr1.fastqH A D08-Mar-2021100 2120

testBam2FastQCoordChr1Pos76.fastqH A D08-Mar-202122 54

testBam2FastQCoordNoCompBase.fastqH A D08-Mar-2021390 2928

testBam2FastQCoordNoCompBase_1.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoordNoCompSecond.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoordNoRG.fastqH A D08-Mar-2021390 2928

testBam2FastQCoordNoRG.listH A D08-Mar-2021211 43

testBam2FastQCoordNoRG_1.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoordNoRG_2.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoordPlus.fastqH A D08-Mar-2021402 2928

testBam2FastQCoordPlus_1.fastqH A D08-Mar-20211.2 KiB8180

testBam2FastQCoordPlus_2.fastqH A D08-Mar-20211.2 KiB8180

testBam2FastQCoordRG.listH A D08-Mar-2021431 65

testBam2FastQCoordRG.rg1.fastqH A D08-Mar-2021390 2928

testBam2FastQCoordRG.rg1_1.fastqH A D08-Mar-2021805 5756

testBam2FastQCoordRG.rg1_2.fastqH A D08-Mar-2021805 5756

testBam2FastQCoordRG.rg2_1.fastqH A D08-Mar-2021230 1716

testBam2FastQCoordRG.rg2_2.fastqH A D08-Mar-2021230 1716

testBam2FastQCoordRG_1.fastqH A D08-Mar-2021116 98

testBam2FastQCoordRG_2.fastqH A D08-Mar-2021116 98

testBam2FastQCoordRGgz.listH A D08-Mar-2021468 65

testBam2FastQCoordRGgz.rg1_2.fastqH A D08-Mar-2021805 5756

testBam2FastQCoordRGi.listH A D08-Mar-2021499 65

testBam2FastQCoordRGi.rg1_interleaved.fastqH A D08-Mar-20211.6 KiB113112

testBam2FastQCoordRGi.rg2_interleaved.fastqH A D08-Mar-2021460 3332

testBam2FastQCoordRGi_interleaved.fastqH A D08-Mar-2021232 1716

testBam2FastQCoord_1.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoord_2.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQCoord_interleaved.fastqH A D08-Mar-20212.2 KiB161160

testBam2FastQReadName.fastqH A D08-Mar-2021110 98

testBam2FastQReadNameAll1.fastqH A D08-Mar-20211.7 KiB121120

testBam2FastQReadNameNoCompBase_2.fastqH A D08-Mar-2021850 5756

testBam2FastQReadNameNoCompFirst.fastqH A D08-Mar-2021850 5756

testBam2FastQReadNameNoCompUnpaired.fastqH A D08-Mar-2021112 98

testBam2FastQReadNameNoRG.fastqH A D08-Mar-2021110 98

testBam2FastQReadNameNoRG.listH A D08-Mar-2021226 43

testBam2FastQReadNameNoRG_1.fastqH A D08-Mar-2021803 5756

testBam2FastQReadNameNoRG_2.fastqH A D08-Mar-2021803 5756

testBam2FastQReadNamePlus.fastqH A D08-Mar-2021112 98

testBam2FastQReadNamePlus_1.fastqH A D08-Mar-2021850 5756

testBam2FastQReadNamePlus_2.fastqH A D08-Mar-2021850 5756

testBam2FastQReadNameRG.listH A D08-Mar-2021455 65

testBam2FastQReadNameRG.rg1.fastqH A D08-Mar-2021110 98

testBam2FastQReadNameRG.rg1_1.fastqH A D08-Mar-2021573 4140

testBam2FastQReadNameRG.rg1_2.fastqH A D08-Mar-2021573 4140

testBam2FastQReadNameRG.rg2_1.fastqH A D08-Mar-2021114 98

testBam2FastQReadNameRG.rg2_2.fastqH A D08-Mar-2021114 98

testBam2FastQReadNameRG_1.fastqH A D08-Mar-2021116 98

testBam2FastQReadNameRG_2.fastqH A D08-Mar-2021116 98

testBam2FastQReadNameRGi.listH A D08-Mar-2021523 65

testBam2FastQReadNameRGi.rg1.fastqH A D08-Mar-2021110 98

testBam2FastQReadNameRGi.rg1_interleaved.fastqH A D08-Mar-20211.1 KiB8180

testBam2FastQReadNameRGi.rg2_interleaved.fastqH A D08-Mar-2021228 1716

testBam2FastQReadNameRGi_interleaved.fastqH A D08-Mar-2021232 1716

testBam2FastQReadNameSO_1.fastqH A D08-Mar-2021803 5756

testBam2FastQReadNameSO_2.fastqH A D08-Mar-2021803 5756

testBam2FastQReadName_1.fastqH A D08-Mar-2021803 5756

testBam2FastQReadName_2.fastqH A D08-Mar-2021803 5756

testBam2FastQReadName_interleaved.fastqH A D08-Mar-20211.6 KiB113112

testClipOverlapCoord.samH A D08-Mar-20214.5 KiB4241

testClipOverlapCoord1.samH A D08-Mar-20214.6 KiB4342

testClipOverlapCoord1Ex0.samH A D08-Mar-20214.6 KiB4342

testClipOverlapCoordClipsOnly.samH A D08-Mar-20213.7 KiB3534

testClipOverlapCoordPool0Clip.samH A D08-Mar-202188 54

testClipOverlapCoordPool3.samH A D08-Mar-20214.3 KiB4241

testClipOverlapCoordPool3Clip.samH A D08-Mar-20214.4 KiB4241

testClipOverlapCoordPool3ClipClipsOnly.samH A D08-Mar-20213.1 KiB3029

testClipOverlapCoordPool3ClipsOnly.samH A D08-Mar-20212.2 KiB2221

testClipOverlapCoordUnmap.samH A D08-Mar-20214.4 KiB4241

testClipOverlapReadName.samH A D08-Mar-20213.8 KiB3534

testClipOverlapReadName1.samH A D08-Mar-20213.9 KiB3635

testClipOverlapReadName1Ex0.samH A D08-Mar-20213.9 KiB3635

testClipOverlapReadNameClipsOnly.samH A D08-Mar-20213.1 KiB2928

testClipOverlapReadNameNoAlphaSortFail.samH A D08-Mar-20213.5 KiB3332

testClipOverlapReadNameNoAlphaSortNoValidate.samH A D08-Mar-20213.8 KiB3534

testDedup.samH A D08-Mar-20212.1 KiB6160

testDedup1.samH A D08-Mar-20212.1 KiB6160

testDedup1Recab.samH A D08-Mar-20212.1 KiB6160

testDedup1Recab.sam.qempH A D08-Mar-2021222 1312

testDedup2Exclude.samH A D08-Mar-20212.1 KiB6160

testDedup2F.samH A D08-Mar-20212.1 KiB6160

testDedup2ForceRecabD.samH A D08-Mar-20212.1 KiB6160

testDedup2ForceRecabD.sam.qempH A D08-Mar-2021312 1817

testDedup2ForceRecabDA.samH A D08-Mar-20212.1 KiB6160

testDedup2RecabF.samH A D08-Mar-20212.1 KiB6160

testDedupRecab.samH A D08-Mar-20212.1 KiB6160

testDedupRecab.sam.qempH A D08-Mar-2021222 1312

testDedupRecabBin.samH A D08-Mar-20212.1 KiB6160

testRecab.samH A D08-Mar-202111.8 KiB206205

testRecab.sam.qempH A D08-Mar-2021310 1615

testRecab.sam.qemp.mapH A D08-Mar-2021310 1615

testRecab2.samH A D08-Mar-20216.7 KiB120119

testRecab2.sam.qempH A D08-Mar-2021478 2625

testRecab2.sam.qemp.mapH A D08-Mar-2021478 2625

testRecab2Keep.samH A D08-Mar-20216.7 KiB120119

testRecab2Keep.sam.qempH A D08-Mar-2021573 3130

testRecab2Keep.sam.qemp.mapH A D08-Mar-2021573 3130

testRecabBin.samH A D08-Mar-202111.8 KiB206205

testRecabBin19.samH A D08-Mar-202111.8 KiB206205

testRecabBin21.samH A D08-Mar-202111.8 KiB206205

testRecabDBSNP.samH A D08-Mar-202111.8 KiB206205

testRecabDBSNP.sam.qempH A D08-Mar-2021212 1211

testRecabDBSNP.sam.qemp.mapH A D08-Mar-2021212 1211

testRecabDBSNPkeepPrev.samH A D08-Mar-202111.8 KiB206205

testRecabDBSNPkeepPrev.sam.qempH A D08-Mar-2021294 1615

testRecabDBSNPkeepPrev.sam.qemp.mapH A D08-Mar-2021294 1615

testRecabFast.sam.qempH A D08-Mar-2021310 1615

testRecabFast.sam.qemp.mapH A D08-Mar-2021310 1615

testRecabMaxQual49.samH A D08-Mar-20217.6 MiB130,001130,000

testRecabMaxQual50.samH A D08-Mar-20217.6 MiB130,001130,000

testRecabMaxQual51.samH A D08-Mar-20217.6 MiB130,001130,000

testRecabMaxQual51.sam.qempH A D08-Mar-2021120 65

testRecabMaxQual51.sam.qemp.mapH A D08-Mar-2021120 65

testRecabMinQual28.samH A D08-Mar-20217.6 MiB130,001130,000

testRecabMinQual28.sam.qempH A D08-Mar-202196 54

testRecabMinQual28.sam.qemp.mapH A D08-Mar-202196 54

testRecabStoreQ.samH A D08-Mar-202111.8 KiB206205

testRecabUseBadOQ.samH A D08-Mar-202111.8 KiB206205

testRecabUseBadOQ.sam.qempH A D08-Mar-2021353 1918

testRecabUseBadOQ.sam.qemp.mapH A D08-Mar-2021353 1918

testRecabUseOQ.samH A D08-Mar-202111.8 KiB206205

testRecabUseOQ.sam.qempH A D08-Mar-2021267 1413

testRecabUseOQ.sam.qemp.mapH A D08-Mar-2021267 1413

testRecabUseStoreOQ.samH A D08-Mar-202111.8 KiB206205

testTags.errH A D08-Mar-2021421 108

testTags.samH A D08-Mar-20211.8 KiB2524

testTagsBam2Bam.errH A D08-Mar-202160 42

trimSam.samH A D08-Mar-20211.3 KiB3837

trimSam3.samH A D08-Mar-20211.3 KiB3837

trimSamL1R2.samH A D08-Mar-20211.3 KiB3837

trimSamL1R2is.samH A D08-Mar-20211.3 KiB3837