| /dports/biology/vcflib/vcflib-1.0.2/smithwaterman/ |
| H A D | LeftAlign.cpp | 44 string softBegin; in leftAlign() local
73 softBegin = querySequence.substr(0, l); in leftAlign()
341 int softdiff = softBegin.size(); in leftAlign()
342 if (!softBegin.empty()) { // remove soft clips if we can in leftAlign()
343 if (flankingLength < softBegin.size()) { in leftAlign()
344 softBegin = softBegin.substr(0, flankingLength - softBegin.size()); in leftAlign()
345 softdiff -= softBegin.size(); in leftAlign()
347 softBegin.clear(); in leftAlign()
634 if (!softBegin.empty()) { in leftAlign()
635 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
[all …]
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/ |
| H A D | LeftAlign.cpp | 44 string softBegin; in leftAlign() local
73 softBegin = querySequence.substr(0, l); in leftAlign()
341 int softdiff = softBegin.size(); in leftAlign()
342 if (!softBegin.empty()) { // remove soft clips if we can in leftAlign()
343 if (flankingLength < softBegin.size()) { in leftAlign()
344 softBegin = softBegin.substr(0, flankingLength - softBegin.size()); in leftAlign()
345 softdiff -= softBegin.size(); in leftAlign()
347 softBegin.clear(); in leftAlign()
634 if (!softBegin.empty()) { in leftAlign()
635 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
[all …]
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| /dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/ |
| H A D | LeftAlign.cpp | 44 string softBegin; in leftAlign() local
73 softBegin = querySequence.substr(0, l); in leftAlign()
341 int softdiff = softBegin.size(); in leftAlign()
342 if (!softBegin.empty()) { // remove soft clips if we can in leftAlign()
343 if (flankingLength < softBegin.size()) { in leftAlign()
344 softBegin = softBegin.substr(0, flankingLength - softBegin.size()); in leftAlign()
345 softdiff -= softBegin.size(); in leftAlign()
347 softBegin.clear(); in leftAlign()
634 if (!softBegin.empty()) { in leftAlign()
635 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
[all …]
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| /dports/biology/freebayes/freebayes-1.3.5/src/ |
| H A D | LeftAlign.cpp | 39 string softBegin; in leftAlign() local
64 alignedReferenceSequence.insert(sp + softBegin.size() + arsOffset, string(l, '-')); in leftAlign()
71 softBegin = alignmentAlignedBases.substr(0, l); in leftAlign()
248 if (!softBegin.empty()) { in leftAlign()
249 newCigar.ADDCIGAR(CIGOP('S', softBegin.size())); in leftAlign()
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfleftalign.cpp | 193 string softBegin; in leftAlign() local
213 alignedReferenceSequence.insert(sp + softBegin.size() + arsOffset, string(l, '-')); in leftAlign()
220 softBegin = alignmentAlignedBases.substr(0, l); in leftAlign()
391 if (!softBegin.empty()) { in leftAlign()
392 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfleftalign.cpp | 184 string softBegin; in leftAlign() local
204 alignedReferenceSequence.insert(sp + softBegin.size() + arsOffset, string(l, '-')); in leftAlign()
211 softBegin = alignmentAlignedBases.substr(0, l); in leftAlign()
382 if (!softBegin.empty()) { in leftAlign()
383 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfleftalign.cpp | 184 string softBegin; in leftAlign() local
204 alignedReferenceSequence.insert(sp + softBegin.size() + arsOffset, string(l, '-')); in leftAlign()
211 softBegin = alignmentAlignedBases.substr(0, l); in leftAlign()
382 if (!softBegin.empty()) { in leftAlign()
383 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign()
|
| /dports/www/firefox-esr/firefox-91.8.0/extensions/spellcheck/src/ |
| H A D | mozInlineSpellWordUtil.cpp | 260 NodeOffset softBegin = NodeOffset(aPositionNode, aPositionOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
326 NodeOffset softBegin = 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 | 260 NodeOffset softBegin = NodeOffset(aPositionNode, aPositionOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
326 NodeOffset softBegin = 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 | 260 NodeOffset softBegin = NodeOffset(aPositionNode, aPositionOffset); in SetPositionAndEnd() local
269 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in SetPositionAndEnd()
326 NodeOffset softBegin = pt; in GetRangeForWord() local
328 nsresult rv = EnsureWords(std::move(softBegin), std::move(softEnd)); in GetRangeForWord()
|