| /dports/biology/bedtools/bedtools2-2.30.0/src/pairToBed/ |
| H A D | pairToBedMain.cpp | 45 bool diffStrand = false; in pairtobed_main() local
117 diffStrand = true; in pairtobed_main()
143 && (sameStrand || diffStrand) ) { in pairtobed_main()
153 if (sameStrand && diffStrand) { in pairtobed_main()
160 searchType, sameStrand, diffStrand, inputIsBam, in pairtobed_main()
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| H A D | pairToBed.h | 46 …string searchType, bool sameStrand, bool diffStrand, bool bamInput, bool bamOutput, bool uncompres…
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| H A D | pairToBed.cpp | 37 string searchType, bool sameStrand, bool diffStrand, bool bamInput, in BedIntersectPE() argument
44 _diffStrand = diffStrand; in BedIntersectPE()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/annotateBed/ |
| H A D | annotateMain.cpp | 36 bool diffStrand = false; in annotate_main() local
109 diffStrand = true; in annotate_main()
122 if (sameStrand && diffStrand) { in annotate_main()
128 …BedAnnotate *ba = new BedAnnotate(mainFile, inputFiles, inputTitles, sameStrand, diffStrand, repor… in annotate_main()
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| H A D | annotateBed.h | 34 …const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool report…
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| H A D | annotateBed.cpp | 17 …const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool report… in BedAnnotate() argument
23 _diffStrand(diffStrand), in BedAnnotate()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/bedFile/ |
| H A D | bedFile.cpp | 340 bool diffStrand, float overlapFraction, in allHits() argument
375 if ( (sameStrand == false && diffStrand == false) in allHits()
379 (diffStrand == true && strands_are_same == false) in allHits()
399 bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal) { in anyHits() argument
433 if ( (sameStrand == false && diffStrand == false) in anyHits()
437 (diffStrand == true && strands_are_same == false) in anyHits()
457 void BedFile::countHits(const BED &a, bool sameStrand, bool diffStrand, bool countsOnly) { in countHits() argument
479 (diffStrand == true && strands_are_same == true) in countHits()
546 (diffStrand == true && strands_are_same == true) in countSplitHits()
589 void BedFile::countListHits(const BED &a, int index, bool sameStrand, bool diffStrand) { in countListHits() argument
[all …]
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| H A D | bedFile.h | 446 vector<BED> &hits, bool sameStrand, bool diffStrand,
451 bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal);
458 bool diffStrand = false, bool countsOnly = false);
466 bool diffStrand = false, bool countsOnly = false);
472 bool sameStrand, bool diffStrand);
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| /dports/biology/bedtools/bedtools2-2.30.0/src/tagBam/ |
| H A D | tagBamMain.cpp | 43 bool diffStrand = false; in tagbam_main() local
120 diffStrand = true; in tagbam_main()
151 if (sameStrand && diffStrand) { in tagbam_main()
188 useIntervals, sameStrand, diffStrand, in tagbam_main()
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| H A D | tagBam.cpp | 19 bool sameStrand, bool diffStrand, float overlapFraction): in TagBam() argument
29 _diffStrand(diffStrand), in TagBam()
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| H A D | tagBam.h | 44 bool diffStrand, float overlapFraction);
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| /dports/biology/bedtools/bedtools2-2.30.0/src/multiBamCov/ |
| H A D | multiBamCovMain.cpp | 45 bool diffStrand = false; in multibamcov_main() local
122 diffStrand = true; in multibamcov_main()
136 diffStrand, overlapFraction, in multibamcov_main()
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| H A D | multiBamCov.cpp | 24 bool diffStrand, float overlapFraction, in MultiCovBam() argument
35 _diffStrand(diffStrand), in MultiCovBam()
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| H A D | multiBamCov.h | 38 bool diffStrand, float overlapFraction,
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/FileRecordTools/Records/ |
| H A D | Record.cpp | 133 bool diffStrand, in intersects() argument
145 sameStrand, diffStrand, in intersects()
152 bool diffStrand, in sameChromIntersects() argument
174 if (diffStrand && !isDiffStrand) { in sameChromIntersects()
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| H A D | Record.h | 137 bool diffStrand,
149 bool diffStrand,
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/chromsweep/ |
| H A D | chromsweep.cpp | 22 bool sameStrand, bool diffStrand, in ChromSweep() argument
31 , _diffStrand(diffStrand) in ChromSweep()
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| H A D | chromsweep.h | 35 bool sameStrand = false, bool diffStrand = false,
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