| /dports/biology/vcflib/vcflib-1.0.2/smithwaterman/ |
| H A D | LeftAlign.cpp | 45 string softEnd; in leftAlign() local
77 softEnd = querySequence.substr(querySequence.size() - l, l); in leftAlign()
402 if (!softEnd.empty()) { // remove soft clips if we can in leftAlign()
403 if (flankingLength < softEnd.size()) { in leftAlign()
404 softEnd = softEnd.substr(flankingLength - softEnd.size()); in leftAlign()
406 softEnd.clear(); in leftAlign()
643 if (!softEnd.empty()) { in leftAlign()
644 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
726 if (!softEnd.empty()) { in leftAlign()
727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign()
[all …]
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/ |
| H A D | LeftAlign.cpp | 45 string softEnd; in leftAlign() local
77 softEnd = querySequence.substr(querySequence.size() - l, l); in leftAlign()
402 if (!softEnd.empty()) { // remove soft clips if we can in leftAlign()
403 if (flankingLength < softEnd.size()) { in leftAlign()
404 softEnd = softEnd.substr(flankingLength - softEnd.size()); in leftAlign()
406 softEnd.clear(); in leftAlign()
643 if (!softEnd.empty()) { in leftAlign()
644 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
726 if (!softEnd.empty()) { in leftAlign()
727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign()
[all …]
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| /dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/ |
| H A D | LeftAlign.cpp | 45 string softEnd; in leftAlign() local
77 softEnd = querySequence.substr(querySequence.size() - l, l); in leftAlign()
402 if (!softEnd.empty()) { // remove soft clips if we can in leftAlign()
403 if (flankingLength < softEnd.size()) { in leftAlign()
404 softEnd = softEnd.substr(flankingLength - softEnd.size()); in leftAlign()
406 softEnd.clear(); in leftAlign()
643 if (!softEnd.empty()) { in leftAlign()
644 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
726 if (!softEnd.empty()) { in leftAlign()
727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign()
[all …]
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| /dports/biology/freebayes/freebayes-1.3.5/src/ |
| H A D | LeftAlign.cpp | 40 string softEnd; in leftAlign() local
74 softEnd = alignmentAlignedBases.substr(alignmentAlignedBases.size() - l, l); in leftAlign()
301 if (!softEnd.empty()) { in leftAlign()
302 newCigar.ADDCIGAR(CIGOP('S', softEnd.size())); in leftAlign()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ |
| H A D | OverhangFixingManager.java | 404 int softEnd = read.getSoftEnd(); in setRead() local
406 if ( ! read.isUnmapped() && softStart < softEnd) { in setRead()
407 … unclippedLoc = genomeLocParser.createGenomeLoc(read.getContig(), softStart, softEnd); in setRead()
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfleftalign.cpp | 194 string softEnd; in leftAlign() local
223 softEnd = alignmentAlignedBases.substr(alignmentAlignedBases.size() - l, l); in leftAlign()
428 if (!softEnd.empty()) { in leftAlign()
429 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ReadUtils.java | 650 int softEnd = read.getEnd(); in getSoftEnd() local
657 softEnd += cig.getLength(); in getSoftEnd()
664 softEnd = read.getEnd(); in getSoftEnd()
666 return softEnd; in getSoftEnd()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfleftalign.cpp | 185 string softEnd; in leftAlign() local
214 softEnd = alignmentAlignedBases.substr(alignmentAlignedBases.size() - l, l); in leftAlign()
419 if (!softEnd.empty()) { in leftAlign()
420 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfleftalign.cpp | 185 string softEnd; in leftAlign() local
214 softEnd = alignmentAlignedBases.substr(alignmentAlignedBases.size() - l, l); in leftAlign()
419 if (!softEnd.empty()) { in leftAlign()
420 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign()
|
| /dports/www/firefox-esr/firefox-91.8.0/extensions/spellcheck/src/ |
| H A D | mozInlineSpellWordUtil.cpp | 267 NodeOffset softEnd = NodeOffset(aEndNode, aEndOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
327 NodeOffset softEnd = pt; in GetRangeForWord() local
328 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in GetRangeForWord()
|
| /dports/www/firefox/firefox-99.0/extensions/spellcheck/src/ |
| H A D | mozInlineSpellWordUtil.cpp | 267 NodeOffset softEnd = NodeOffset(aEndNode, aEndOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
327 NodeOffset softEnd = pt; in GetRangeForWord() local
328 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in GetRangeForWord()
|
| /dports/mail/thunderbird/thunderbird-91.8.0/extensions/spellcheck/src/ |
| H A D | mozInlineSpellWordUtil.cpp | 267 NodeOffset softEnd = NodeOffset(aEndNode, aEndOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
327 NodeOffset softEnd = pt; in GetRangeForWord() local
328 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in GetRangeForWord()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/recalibration/ |
| H A D | BaseRecalibrationEngine.java | 336 final int softEnd = read.getSoftEnd();
338 if (knownSite.getEnd() < softStart || knownSite.getStart() > softEnd) {
|