diff --git a/._Makefile.uZs1Vt b/._Makefile.uZs1Vt new file mode 100755 index 0000000000000000000000000000000000000000..24eac48d99a877e496a2e799c98d61e4cd399501 Binary files /dev/null and b/._Makefile.uZs1Vt differ diff --git a/._README.89gPvU b/._README.89gPvU new file mode 100755 index 0000000000000000000000000000000000000000..92241a843c2ab0477beec047980afd7fc1a0d2ca Binary files /dev/null and b/._README.89gPvU differ diff --git a/src/intersectBed/._Makefile.tfyeHx b/src/intersectBed/._Makefile.tfyeHx new file mode 100755 index 0000000000000000000000000000000000000000..0240bfb2dd110306be5f8c7a2043a094a60f6400 Binary files /dev/null and b/src/intersectBed/._Makefile.tfyeHx differ diff --git a/src/intersectBed/._genes.gff2.aEfWZN b/src/intersectBed/._genes.gff2.aEfWZN new file mode 100644 index 0000000000000000000000000000000000000000..8da5d29039671ebde8bbd071ddc146511022f323 Binary files /dev/null and b/src/intersectBed/._genes.gff2.aEfWZN differ diff --git a/src/intersectBed/._intersectBed.cpp.oBliXV b/src/intersectBed/._intersectBed.cpp.oBliXV new file mode 100755 index 0000000000000000000000000000000000000000..3c5508c2ed5a5423947990c9dc820376413d2d13 Binary files /dev/null and b/src/intersectBed/._intersectBed.cpp.oBliXV differ diff --git a/src/intersectBed/._intersectBed.h.HbGRhQ b/src/intersectBed/._intersectBed.h.HbGRhQ new file mode 100755 index 0000000000000000000000000000000000000000..c7cfbe512593fd62dbb3fddd543b289c7a455c4c Binary files /dev/null and b/src/intersectBed/._intersectBed.h.HbGRhQ differ diff --git a/src/intersectBed/._intersectMain.cpp.bSv9Uk b/src/intersectBed/._intersectMain.cpp.bSv9Uk new file mode 100755 index 0000000000000000000000000000000000000000..4ddcee7a88ce028c8467501295f17856225a63bb Binary files /dev/null and b/src/intersectBed/._intersectMain.cpp.bSv9Uk differ diff --git a/src/linksBed/._Makefile.gpikGf b/src/linksBed/._Makefile.gpikGf new file mode 100755 index 0000000000000000000000000000000000000000..862320edcae751cc518fb86118e1c2ac9f419a99 Binary files /dev/null and b/src/linksBed/._Makefile.gpikGf differ diff --git a/src/linksBed/._linksBed.cpp.2dulZX b/src/linksBed/._linksBed.cpp.2dulZX new file mode 100755 index 0000000000000000000000000000000000000000..bbbb64227f0d6b8f2a965f30da8a2a605aa5ff25 Binary files /dev/null and b/src/linksBed/._linksBed.cpp.2dulZX differ diff --git a/src/linksBed/._linksBed.h.8ODgDj b/src/linksBed/._linksBed.h.8ODgDj new file mode 100755 index 0000000000000000000000000000000000000000..069ada5bf14f6c20f868bef0ccccbcf1607628bb Binary files /dev/null and b/src/linksBed/._linksBed.h.8ODgDj differ diff --git a/src/linksBed/._linksMain.cpp.Vv0SnB b/src/linksBed/._linksMain.cpp.Vv0SnB new file mode 100755 index 0000000000000000000000000000000000000000..295d6cf35fc231b256160060c9997ea9cb9552f3 Binary files /dev/null and b/src/linksBed/._linksMain.cpp.Vv0SnB differ diff --git a/src/maskFastaFromBed/._Makefile.Fi5w6K b/src/maskFastaFromBed/._Makefile.Fi5w6K new file mode 100755 index 0000000000000000000000000000000000000000..44ca87065f435e1394cef3cef413589f2e1d0bef Binary files /dev/null and b/src/maskFastaFromBed/._Makefile.Fi5w6K differ diff --git a/src/maskFastaFromBed/._maskFastaFromBed.cpp.1aARb4 b/src/maskFastaFromBed/._maskFastaFromBed.cpp.1aARb4 new file mode 100755 index 0000000000000000000000000000000000000000..60e2c0dc5c48a8e098dc1906d713578e417793fb Binary files /dev/null and b/src/maskFastaFromBed/._maskFastaFromBed.cpp.1aARb4 differ diff --git a/src/maskFastaFromBed/._maskFastaFromBed.h.ArCWdS b/src/maskFastaFromBed/._maskFastaFromBed.h.ArCWdS new file mode 100755 index 0000000000000000000000000000000000000000..ea84ba8758981eb0bf2362f6f10fa3c9d3b8eba2 Binary files /dev/null and b/src/maskFastaFromBed/._maskFastaFromBed.h.ArCWdS differ diff --git a/src/maskFastaFromBed/._maskFastaFromBedMain.cpp.jTrlLO b/src/maskFastaFromBed/._maskFastaFromBedMain.cpp.jTrlLO new file mode 100755 index 0000000000000000000000000000000000000000..214cd1b0978cea42aef13181dac525e2fe8e5dc4 Binary files /dev/null and b/src/maskFastaFromBed/._maskFastaFromBedMain.cpp.jTrlLO differ diff --git a/src/mergeBed/._Makefile.smGUij b/src/mergeBed/._Makefile.smGUij new file mode 100755 index 0000000000000000000000000000000000000000..5882517d2059358c6736a407ccde71d4d0fa568f Binary files /dev/null and b/src/mergeBed/._Makefile.smGUij differ diff --git a/src/mergeBed/._mergeBed.cpp.IsVQ8P b/src/mergeBed/._mergeBed.cpp.IsVQ8P new file mode 100755 index 0000000000000000000000000000000000000000..69bf3b99f6058e90ec7e1560e9b3fb99ca7d2839 Binary files /dev/null and b/src/mergeBed/._mergeBed.cpp.IsVQ8P differ diff --git a/src/mergeBed/._mergeBed.h.xdU0yO b/src/mergeBed/._mergeBed.h.xdU0yO new file mode 100755 index 0000000000000000000000000000000000000000..02c7405a6208da4296843931d14c801e2bc8fcf1 Binary files /dev/null and b/src/mergeBed/._mergeBed.h.xdU0yO differ diff --git a/src/mergeBed/._mergeMain.cpp.YydplS b/src/mergeBed/._mergeMain.cpp.YydplS new file mode 100755 index 0000000000000000000000000000000000000000..33a320f85b32f4dfaf37bf9b5f0a86e7e64cea3c Binary files /dev/null and b/src/mergeBed/._mergeMain.cpp.YydplS differ diff --git a/src/pairToBed/._Makefile.351twO b/src/pairToBed/._Makefile.351twO new file mode 100755 index 0000000000000000000000000000000000000000..13e0b9d963f707c4157c8e0bf9f1b60bca8bf022 Binary files /dev/null and b/src/pairToBed/._Makefile.351twO differ diff --git a/src/pairToBed/._pairToBed.cpp.L7PQHJ b/src/pairToBed/._pairToBed.cpp.L7PQHJ new file mode 100755 index 0000000000000000000000000000000000000000..41ea2004a454f3227de8cc422e92fd05e7e13ce8 Binary files /dev/null and b/src/pairToBed/._pairToBed.cpp.L7PQHJ differ diff --git a/src/pairToBed/._pairToBed.h.Tsyifc b/src/pairToBed/._pairToBed.h.Tsyifc new file mode 100755 index 0000000000000000000000000000000000000000..8915a3cbcd54c0c7e7237e05194cd3d3bc20132a Binary files /dev/null and b/src/pairToBed/._pairToBed.h.Tsyifc differ diff --git a/src/pairToBed/._pairToBedMain.cpp.gOUhIO b/src/pairToBed/._pairToBedMain.cpp.gOUhIO new file mode 100755 index 0000000000000000000000000000000000000000..9c51b9af31cdf0eaf200fa9b175dc97fdf0f8e39 Binary files /dev/null and b/src/pairToBed/._pairToBedMain.cpp.gOUhIO differ diff --git a/src/pairToBed/test b/src/pairToBed/test index e24fae230d2db3630e113e169dfe9dfdb166f3a0..2fba56617660d2f7696cb60957e31262e489bc9b 100644 Binary files a/src/pairToBed/test and b/src/pairToBed/test differ diff --git a/src/pairToPair/._Makefile.mlHLKb b/src/pairToPair/._Makefile.mlHLKb new file mode 100755 index 0000000000000000000000000000000000000000..1fd1d4f2bfde63f93f62943c2e09bc15764bf42e Binary files /dev/null and b/src/pairToPair/._Makefile.mlHLKb differ diff --git a/src/pairToPair/._pairToPair.cpp.o6hzYp b/src/pairToPair/._pairToPair.cpp.o6hzYp new file mode 100755 index 0000000000000000000000000000000000000000..96004cab8b41a92d796a31897168208af9b5a350 Binary files /dev/null and b/src/pairToPair/._pairToPair.cpp.o6hzYp differ diff --git a/src/pairToPair/._pairToPair.h.DYjZTy b/src/pairToPair/._pairToPair.h.DYjZTy new file mode 100755 index 0000000000000000000000000000000000000000..61f7bd58e0dd176fa8c64d7d8dd60ecbf29d0e06 Binary files /dev/null and b/src/pairToPair/._pairToPair.h.DYjZTy differ diff --git a/src/pairToPair/._pairToPairMain.cpp.aOig3B b/src/pairToPair/._pairToPairMain.cpp.aOig3B new file mode 100755 index 0000000000000000000000000000000000000000..158ea959d44576575bd75e91fb961a45da02f8f5 Binary files /dev/null and b/src/pairToPair/._pairToPairMain.cpp.aOig3B differ diff --git a/src/shuffleBed/._Makefile.MnUedb b/src/shuffleBed/._Makefile.MnUedb new file mode 100755 index 0000000000000000000000000000000000000000..d069628fb3b23ff25f1365b520e38f06e0a5f370 Binary files /dev/null and b/src/shuffleBed/._Makefile.MnUedb differ diff --git a/src/shuffleBed/._shuffleBed.cpp.7m8iqY b/src/shuffleBed/._shuffleBed.cpp.7m8iqY new file mode 100755 index 0000000000000000000000000000000000000000..11f7d6a72e55c7c3d2bf3ee86687548b981e41ee Binary files /dev/null and b/src/shuffleBed/._shuffleBed.cpp.7m8iqY differ diff --git a/src/shuffleBed/._shuffleBed.h.2XpBHZ b/src/shuffleBed/._shuffleBed.h.2XpBHZ new file mode 100755 index 0000000000000000000000000000000000000000..ebf7755a36ae0abd2ed4a4eb3b5123d73eee76e8 Binary files /dev/null and b/src/shuffleBed/._shuffleBed.h.2XpBHZ differ diff --git a/src/shuffleBed/._shuffleBedMain.cpp.dXBQK4 b/src/shuffleBed/._shuffleBedMain.cpp.dXBQK4 new file mode 100755 index 0000000000000000000000000000000000000000..7411b40d36c71c11527aa849dd19b0e1f069dda2 Binary files /dev/null and b/src/shuffleBed/._shuffleBedMain.cpp.dXBQK4 differ diff --git a/src/slopBed/._Makefile.pfRQTp b/src/slopBed/._Makefile.pfRQTp new file mode 100755 index 0000000000000000000000000000000000000000..ac851c6dffc262a9d6253c35fbe0b46c1dec7bb2 Binary files /dev/null and b/src/slopBed/._Makefile.pfRQTp differ diff --git a/src/slopBed/._slopBed.cpp.04OZWb b/src/slopBed/._slopBed.cpp.04OZWb new file mode 100755 index 0000000000000000000000000000000000000000..701eceb2497e0f069ab5d5aef83f8d62c1716502 Binary files /dev/null and b/src/slopBed/._slopBed.cpp.04OZWb differ diff --git a/src/slopBed/._slopBed.h.xri3gY b/src/slopBed/._slopBed.h.xri3gY new file mode 100755 index 0000000000000000000000000000000000000000..ce08b61acf6c104088af593c42d0af5e06e786ac Binary files /dev/null and b/src/slopBed/._slopBed.h.xri3gY differ diff --git a/src/slopBed/._slopBedMain.cpp.yLO4Sq b/src/slopBed/._slopBedMain.cpp.yLO4Sq new file mode 100755 index 0000000000000000000000000000000000000000..9968ab0fc3e3740f76474d74489d39e7f498b557 Binary files /dev/null and b/src/slopBed/._slopBedMain.cpp.yLO4Sq differ diff --git a/src/sortBed/._Makefile.uxcSld b/src/sortBed/._Makefile.uxcSld new file mode 100755 index 0000000000000000000000000000000000000000..36dbf9cde9fe3321df7141f920819d71f10e1fb0 Binary files /dev/null and b/src/sortBed/._Makefile.uxcSld differ diff --git a/src/sortBed/._sortBed.cpp.vYsEEN b/src/sortBed/._sortBed.cpp.vYsEEN new file mode 100755 index 0000000000000000000000000000000000000000..04eca94ac73105632eace6b9f50b9c9866dc9ee2 Binary files /dev/null and b/src/sortBed/._sortBed.cpp.vYsEEN differ diff --git a/src/sortBed/._sortBed.h.xIbyxy b/src/sortBed/._sortBed.h.xIbyxy new file mode 100755 index 0000000000000000000000000000000000000000..5cf43f6c566c951485221d6065801195f489ecd2 Binary files /dev/null and b/src/sortBed/._sortBed.h.xIbyxy differ diff --git a/src/sortBed/._sortMain.cpp.d9D5ch b/src/sortBed/._sortMain.cpp.d9D5ch new file mode 100755 index 0000000000000000000000000000000000000000..2c202cf69abd5ac865e424665fb682426a0aaa32 Binary files /dev/null and b/src/sortBed/._sortMain.cpp.d9D5ch differ diff --git a/src/subtractBed/._Makefile.g9qnS7 b/src/subtractBed/._Makefile.g9qnS7 new file mode 100755 index 0000000000000000000000000000000000000000..5420ff27b53bae7f6881f0bdeb22e4e3ae21d119 Binary files /dev/null and b/src/subtractBed/._Makefile.g9qnS7 differ diff --git a/src/subtractBed/._subtractBed.cpp.GN2oCu b/src/subtractBed/._subtractBed.cpp.GN2oCu new file mode 100755 index 0000000000000000000000000000000000000000..5b990f507b82b05ebd7714f5eaea3fe70be67fa4 Binary files /dev/null and b/src/subtractBed/._subtractBed.cpp.GN2oCu differ diff --git a/src/subtractBed/._subtractBed.h.VBT3bK b/src/subtractBed/._subtractBed.h.VBT3bK new file mode 100755 index 0000000000000000000000000000000000000000..128bafc6058d2f36f36e2ef062b0e8f24e5e4de0 Binary files /dev/null and b/src/subtractBed/._subtractBed.h.VBT3bK differ diff --git a/src/subtractBed/._subtractMain.cpp.25m2T7 b/src/subtractBed/._subtractMain.cpp.25m2T7 new file mode 100755 index 0000000000000000000000000000000000000000..27a993bdd8cfd32f59fd7211c7d0bbe4427799c1 Binary files /dev/null and b/src/subtractBed/._subtractMain.cpp.25m2T7 differ diff --git a/src/utils/BamTools/._BGZF.cpp.bbLHll b/src/utils/BamTools/._BGZF.cpp.bbLHll new file mode 100644 index 0000000000000000000000000000000000000000..3a7f6f5316b851801959ceb96455ebc0a121291a Binary files /dev/null and b/src/utils/BamTools/._BGZF.cpp.bbLHll differ diff --git a/src/utils/BamTools/._BGZF.h.Tuje5n b/src/utils/BamTools/._BGZF.h.Tuje5n new file mode 100644 index 0000000000000000000000000000000000000000..0e15db22ccaa2d62c2fb714d375e0192c74bf913 Binary files /dev/null and b/src/utils/BamTools/._BGZF.h.Tuje5n differ diff --git a/src/utils/BamTools/._BamAux.h.4IdyYm b/src/utils/BamTools/._BamAux.h.4IdyYm new file mode 100644 index 0000000000000000000000000000000000000000..89fd192318266baf377612b37e9aa41a4d7f589c Binary files /dev/null and b/src/utils/BamTools/._BamAux.h.4IdyYm differ diff --git a/src/utils/BamTools/._BamReader.cpp.bRjIIg b/src/utils/BamTools/._BamReader.cpp.bRjIIg new file mode 100644 index 0000000000000000000000000000000000000000..2c73a719addca40d4b37098d20f128a452610c6d Binary files /dev/null and b/src/utils/BamTools/._BamReader.cpp.bRjIIg differ diff --git a/src/utils/BamTools/._BamReader.h.kHWNMK b/src/utils/BamTools/._BamReader.h.kHWNMK new file mode 100644 index 0000000000000000000000000000000000000000..f2a9d66a9a39baf8f0500963d2493cab25dea1ef Binary files /dev/null and b/src/utils/BamTools/._BamReader.h.kHWNMK differ diff --git a/src/utils/BamTools/._BamWriter.cpp.xqjF0p b/src/utils/BamTools/._BamWriter.cpp.xqjF0p new file mode 100644 index 0000000000000000000000000000000000000000..f63d2fee5773d0e891c9d655fd7580507bbdd32a Binary files /dev/null and b/src/utils/BamTools/._BamWriter.cpp.xqjF0p differ diff --git a/src/utils/BamTools/._BamWriter.h.PhZ5dQ b/src/utils/BamTools/._BamWriter.h.PhZ5dQ new file mode 100644 index 0000000000000000000000000000000000000000..ba37913d7465d0f202a5dd76ed5e1f1658f5e6fb Binary files /dev/null and b/src/utils/BamTools/._BamWriter.h.PhZ5dQ differ diff --git a/src/utils/BamTools/._Makefile.fyKutp b/src/utils/BamTools/._Makefile.fyKutp new file mode 100644 index 0000000000000000000000000000000000000000..867c7abc458e9240707783fb4428d5cd3ace503c Binary files /dev/null and b/src/utils/BamTools/._Makefile.fyKutp differ diff --git a/src/utils/BamTools/BGZF.cpp b/src/utils/BamTools/BGZF.cpp index 4fb7878516a892317dfe395f5c3d7073da28c053..d0242d6c7aaab52f6febc80933a016a99fcff55b 100644 --- a/src/utils/BamTools/BGZF.cpp +++ b/src/utils/BamTools/BGZF.cpp @@ -53,16 +53,11 @@ void BgzfData::Close(void) { // flush the BGZF block if ( IsWriteOnly ) { FlushBlock(); } - // write an empty block (as EOF marker) - int blockLength = DeflateBlock(); - fwrite(CompressedBlock, 1, blockLength, Stream); - // flush and close fflush(Stream); fclose(Stream); } - // compresses the current block int BgzfData::DeflateBlock(void) { diff --git a/src/utils/bedFile/._Makefile.8Q3rcz b/src/utils/bedFile/._Makefile.8Q3rcz new file mode 100755 index 0000000000000000000000000000000000000000..35995110138631222510cec9d1e1a0328cf811ad Binary files /dev/null and b/src/utils/bedFile/._Makefile.8Q3rcz differ diff --git a/src/utils/bedFile/._bedFile.cpp.1SOiqV b/src/utils/bedFile/._bedFile.cpp.1SOiqV new file mode 100755 index 0000000000000000000000000000000000000000..2d00304f4bcf6e81ca203d46711f3276fc4f73f7 Binary files /dev/null and b/src/utils/bedFile/._bedFile.cpp.1SOiqV differ diff --git a/src/utils/bedFile/._bedFile.h.7vGaVw b/src/utils/bedFile/._bedFile.h.7vGaVw new file mode 100755 index 0000000000000000000000000000000000000000..9b4eb1333f41fa8baebf969fdb862fe84e8a0d40 Binary files /dev/null and b/src/utils/bedFile/._bedFile.h.7vGaVw differ diff --git a/src/utils/bedFilePE/._Makefile.Je89TI b/src/utils/bedFilePE/._Makefile.Je89TI new file mode 100755 index 0000000000000000000000000000000000000000..9517e63803aab691a31283eb91150ca2c69a5d13 Binary files /dev/null and b/src/utils/bedFilePE/._Makefile.Je89TI differ diff --git a/src/utils/bedFilePE/._bedFilePE.cpp.inqqHF b/src/utils/bedFilePE/._bedFilePE.cpp.inqqHF new file mode 100755 index 0000000000000000000000000000000000000000..7c143e9701d2b8ad4f86dd29882c555af209a8c7 Binary files /dev/null and b/src/utils/bedFilePE/._bedFilePE.cpp.inqqHF differ diff --git a/src/utils/bedFilePE/._bedFilePE.h.2Xtiv7 b/src/utils/bedFilePE/._bedFilePE.h.2Xtiv7 new file mode 100755 index 0000000000000000000000000000000000000000..7343f38fdb15a385dc7fb18013e5b3e44351d688 Binary files /dev/null and b/src/utils/bedFilePE/._bedFilePE.h.2Xtiv7 differ diff --git a/src/utils/lineFileUtilities/._Makefile.GI4MVF b/src/utils/lineFileUtilities/._Makefile.GI4MVF new file mode 100755 index 0000000000000000000000000000000000000000..6aa344fb65ecae65c93489b1d12fe4423df5acd4 Binary files /dev/null and b/src/utils/lineFileUtilities/._Makefile.GI4MVF differ diff --git a/src/utils/lineFileUtilities/._lineFileUtilities.cpp.GfgcED b/src/utils/lineFileUtilities/._lineFileUtilities.cpp.GfgcED new file mode 100755 index 0000000000000000000000000000000000000000..9416c1ce1ff0952935d5c66bf8e8603b28459cc1 Binary files /dev/null and b/src/utils/lineFileUtilities/._lineFileUtilities.cpp.GfgcED differ diff --git a/src/utils/lineFileUtilities/._lineFileUtilities.h.N4NA5H b/src/utils/lineFileUtilities/._lineFileUtilities.h.N4NA5H new file mode 100755 index 0000000000000000000000000000000000000000..97bb04d64902c776bae17a37996651562120a26e Binary files /dev/null and b/src/utils/lineFileUtilities/._lineFileUtilities.h.N4NA5H differ diff --git a/src/windowBed/._Makefile.awpfkQ b/src/windowBed/._Makefile.awpfkQ new file mode 100755 index 0000000000000000000000000000000000000000..ceefab095f9698e0b2a3d217f1b869160ced4778 Binary files /dev/null and b/src/windowBed/._Makefile.awpfkQ differ diff --git a/src/windowBed/._windowBed.cpp.AW1TnX b/src/windowBed/._windowBed.cpp.AW1TnX new file mode 100755 index 0000000000000000000000000000000000000000..8fcb78746e2b3d496b039b558c4cbccf1a8557b9 Binary files /dev/null and b/src/windowBed/._windowBed.cpp.AW1TnX differ diff --git a/src/windowBed/._windowBed.h.RlqruJ b/src/windowBed/._windowBed.h.RlqruJ new file mode 100755 index 0000000000000000000000000000000000000000..e271cf896348ed55480d601323981ea3d5b99cdf Binary files /dev/null and b/src/windowBed/._windowBed.h.RlqruJ differ diff --git a/src/windowBed/._windowMain.cpp.qs7pO6 b/src/windowBed/._windowMain.cpp.qs7pO6 new file mode 100755 index 0000000000000000000000000000000000000000..eecf41da7039f616a04659b29de6607cfb575444 Binary files /dev/null and b/src/windowBed/._windowMain.cpp.qs7pO6 differ