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Searched refs:alignmentLength (Results 1 – 25 of 67) sorted by relevance

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/dports/biology/mothur/mothur-1.46.1/source/calculators/
H A Dfilters.h36 a.assign(alignmentLength, 0); in initialize()
37 t.assign(alignmentLength, 0); in initialize()
38 g.assign(alignmentLength, 0); in initialize()
39 c.assign(alignmentLength, 0); in initialize()
40 gap.assign(alignmentLength, 0); in initialize()
46 for(int i=0;i<alignmentLength;i++){ in doSoft()
52 for(int i=0;i<alignmentLength;i++){ in mergeFilter()
61 for(int i=0;i<alignmentLength;i++){ in doVertical()
69 for(int i=0;i<alignmentLength;i++){ in doVerticalAllBases()
113 for(int j=0;j<alignmentLength;j++){ in getFreqs()
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/dports/biology/mothur/mothur-1.46.1/source/chimera/
H A Dchimerarealigner.cpp24 alignmentLength = query->getAlignLength(); //x in reAlign()
46 profile.resize(alignmentLength); in buildTemplateProfile()
51 for(int j=0;j<alignmentLength;j++){ in buildTemplateProfile()
65 for(int i=0;i<alignmentLength;i++){ in buildTemplateProfile()
82 alignMatrix.resize(alignmentLength+1); in createAlignMatrix()
83 for(int i=0;i<=alignmentLength;i++){ in createAlignMatrix()
165 string queryAlignment(alignmentLength, '.'); in getNewAlignment()
166 string referenceAlignment(alignmentLength, '.'); in getNewAlignment()
199 if(currentRow < alignmentLength){ in getNewAlignment()
200 for(int i=alignmentLength;i>currentRow;i--){ in getNewAlignment()
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/dports/biology/canu/canu-2.2/src/correction/
H A DfalconConsensus-alignTag.C381 char *tAln = new char [align.alignmentLength + 1]; in alignReadsToTemplate()
382 char *rAln = new char [align.alignmentLength + 1]; in alignReadsToTemplate()
385 align.alignmentLength, in alignReadsToTemplate()
410 if (tAln[align.alignmentLength - ii - 1] != '-') teSkip++; in alignReadsToTemplate()
411 if (rAln[align.alignmentLength - ii - 1] != '-') reSkip++; in alignReadsToTemplate()
426 printLog(evidence, j, " full template ...%100.100s\n", tAln + align.alignmentLength - 100); in alignReadsToTemplate()
427 printLog(evidence, j, " full evidence ...%100.100s\n", rAln + align.alignmentLength - 100); in alignReadsToTemplate()
430 tAln[align.alignmentLength - eSkip] = 0; // Truncate the alignment strings for printing. in alignReadsToTemplate()
431 rAln[align.alignmentLength - eSkip] = 0; in alignReadsToTemplate()
443 if (align.alignmentLength > bSkip + eSkip + 500) in alignReadsToTemplate()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/
H A DAdapterTrimTransformer.java42 int alignmentLength = minClipLength; in apply() local
46 for (int j = 0; j < alignmentLength; j++) { in apply()
57 …alignmentLength = alignmentLength < adapterSequence.length() ? alignmentLength + 1 : alignmentLeng… in apply()
/dports/biology/canu/canu-2.2/src/utility/src/utility/
H A Dedlib.C183 result.alignmentLength = 0; in edlibAlign()
341 for (int i = 0; i <= alignmentLength; i++) { in edlibAlignmentToCigar()
354 if (i < alignmentLength) { in edlibAlignmentToCigar()
363 if (i < alignmentLength) { in edlibAlignmentToCigar()
435 qry_aln_str[alignmentLength] = tgt_aln_str[alignmentLength] = '\0'; in edlibAlignmentToStrings()
436 assert(strlen(qry_aln_str) == alignmentLength && strlen(tgt_aln_str) == alignmentLength); in edlibAlignmentToStrings()
479 qryAln[result.alignmentLength] = 0; in edlibAlignmentToStrings()
480 tgtAln[result.alignmentLength] = 0; in edlibAlignmentToStrings()
482 assert(strlen(qryAln) == result.alignmentLength); in edlibAlignmentToStrings()
483 assert(strlen(tgtAln) == result.alignmentLength); in edlibAlignmentToStrings()
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H A Dedlib.H200 int alignmentLength; member
253 char* edlibAlignmentToCigar(const unsigned char* alignment, int alignmentLength,
257 uint32 alignmentLength,
265 void edlibAlignmentToStrings(const unsigned char* alignment, int alignmentLength,
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dfilterseqscommand.cpp187 alignmentLength = testSeq.getAlignLength(); in execute()
221 for(int i=0;i<alignmentLength;i++){ in execute()
421 F.setLength(alignmentLength); in createFilter()
426 else { F.setFilter(string(alignmentLength, '1')); } in createFilter()
456 params->F.setLength(params->alignmentLength); in driverCreateFilter()
562 for (int k = 0; k < alignmentLength; k++) { F.a[k] += dataBundle->F.a[k]; } in createProcessesCreateFilter()
563 for (int k = 0; k < alignmentLength; k++) { F.t[k] += dataBundle->F.t[k]; } in createProcessesCreateFilter()
564 for (int k = 0; k < alignmentLength; k++) { F.g[k] += dataBundle->F.g[k]; } in createProcessesCreateFilter()
565 for (int k = 0; k < alignmentLength; k++) { F.c[k] += dataBundle->F.c[k]; } in createProcessesCreateFilter()
566 for (int k = 0; k < alignmentLength; k++) { F.gap[k] += dataBundle->F.gap[k]; } in createProcessesCreateFilter()
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H A Dfilterseqscommand.h41 int alignmentLength, processors; variable
63 int alignmentLength, threadid; member
80 alignmentLength = aLength; in filterData()
93 int alignmentLength; member
110 alignmentLength = aLength; in filterRunData()
/dports/biology/edlib/edlib-d5774b4/apps/aligner/
H A Daligner.cpp18 const unsigned char* alignment, const int alignmentLength,
155 unsigned char* alignment = NULL; int alignmentLength; in main() local
179 alignmentLength = result.alignmentLength; in main()
206 printAlignment(query, target, alignment, alignmentLength, in main()
212 char* cigar =edlibAlignmentToCigar(alignment, alignmentLength, cigarFormat); in main()
332 const unsigned char* alignment, const int alignmentLength, in printAlignment() argument
338 for (int i = 0; i < alignmentLength; i++) { in printAlignment()
343 for (int start = 0; start < alignmentLength; start += 50) { in printAlignment()
347 for (int j = start; j < start + 50 && j < alignmentLength; j++) { in printAlignment()
359 for (int j = start; j < start + 50 && j < alignmentLength; j++) { in printAlignment()
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/dports/biology/canu/canu-2.2/src/overlapAlign/
H A DcomputeOverlapAlignment.C43 (pp >= result.alignmentLength)) in getScore()
144 char *aAln = new char [result.alignmentLength + 1]; in extend5()
145 char *bAln = new char [result.alignmentLength + 1]; in extend5()
296 char *aAln = new char [result.alignmentLength + 1]; in extend3()
297 char *bAln = new char [result.alignmentLength + 1]; in extend3()
346 for (; ii < result.alignmentLength; ii++) { in extend3()
461 alignLen = result.alignmentLength; in computeAlignment()
467 result.alignmentLength, in computeAlignment()
477 result.alignmentLength, in computeAlignment()
785 char *baln = new char [result.alignmentLength + 1]; in computeOverlapAlignment()
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/dports/biology/canu/canu-2.2/src/overlapInCore/
H A Dedalign.C66 … result.alignmentLength, (1) ? EDLIB_CIGAR_STANDARD : EDLIB_CIGAR_EXTENDED); in pairAlign()
79 100.0 - 100.0 * result.editDistance / result.alignmentLength, in pairAlign()
130 … result.alignmentLength, (1) ? EDLIB_CIGAR_STANDARD : EDLIB_CIGAR_EXTENDED); in refAlign()
141 …edlibAlignmentAnalyze(result.alignment, result.alignmentLength, nMatch, nMismatch, nInsertOpen, nI… in refAlign()
148 result.alignmentLength, in refAlign()
149 100.0 - 100.0 * result.editDistance / result.alignmentLength, in refAlign()
150 100.0 * (nInsertOpen + nDeleteOpen) / result.alignmentLength, in refAlign()
151 100.0 * (nInsert + nDelete) / result.alignmentLength, in refAlign()
/dports/biology/edlib/edlib-d5774b4/edlib/src/
H A Dedlib.cpp111 unsigned char** alignment, int* alignmentLength);
117 unsigned char** alignment, int* alignmentLength);
150 result.alignmentLength = 0; in edlibAlign()
314 for (int i = 0; i <= alignmentLength; i++) { in edlibAlignmentToCigar()
327 if (i < alignmentLength) { in edlibAlignmentToCigar()
336 if (i < alignmentLength) { in edlibAlignmentToCigar()
952 *alignmentLength = 0; in obtainAlignmentTraceback()
1133 (*alignment)[(*alignmentLength)++] = moveCode; in obtainAlignmentTraceback()
1142 reverse(*alignment, *alignment + (*alignmentLength)); in obtainAlignmentTraceback()
1172 *alignmentLength = targetLength + queryLength; in obtainAlignment()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Devaluate_alignment.h127 unsigned alignmentLength; member
138 … alignmentLength(0), alignmentSimilarity(0.0), alignmentIdentity(0.0), alignmentScore(0) in AlignmentStats()
175 stats.alignmentLength = 0; in clear()
299 stats.alignmentLength = length(row0); in computeAlignmentStats()
301 / static_cast<float>(stats.alignmentLength); in computeAlignmentStats()
303 / static_cast<float>(stats.alignmentLength); in computeAlignmentStats()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Devaluate_alignment.h127 unsigned alignmentLength; member
138 … alignmentLength(0), alignmentSimilarity(0.0), alignmentIdentity(0.0), alignmentScore(0) in AlignmentStats()
175 stats.alignmentLength = 0; in clear()
299 stats.alignmentLength = length(row0); in computeAlignmentStats()
301 / static_cast<float>(stats.alignmentLength); in computeAlignmentStats()
303 / static_cast<float>(stats.alignmentLength); in computeAlignmentStats()
/dports/biology/canu/canu-2.2/src/utgcns/
H A DunitigConsensus.C528 result.alignmentLength, in generateTemplateStitch()
684 if (align.alignmentLength > 0) { in alignEdLib()
731 if (align.alignmentLength > 0) { in alignEdLib()
747 char *tgtaln = new char [align.alignmentLength+1]; in alignEdLib()
748 char *qryaln = new char [align.alignmentLength+1]; in alignEdLib()
750 memset(tgtaln, 0, sizeof(char) * (align.alignmentLength+1)); in alignEdLib()
778 aln.qstr = new char [align.alignmentLength + nMatch + 1]; in alignEdLib()
779 aln.tstr = new char [align.alignmentLength + nMatch + 1]; in alignEdLib()
781 for (uint32 ii=0, jj=0; ii<align.alignmentLength; ii++) { in alignEdLib()
1031 int alignmentLength, in edlibAlignmentToCanu() argument
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/dports/biology/edlib/edlib-d5774b4/test/
H A DrunTests.cpp24 unsigned char* alignment, int alignmentLength);
26 int getAlignmentStart(const unsigned char* alignment, int alignmentLength,
122 result.alignment, result.alignmentLength)) { in runRandomTests()
126 int alignmentStart = getAlignmentStart(result.alignment, result.alignmentLength, in runRandomTests()
180 mode, result3.alignment, result3.alignmentLength)) { in runRandomTests()
250 result.alignment, result.alignmentLength)) { in executeTest()
595 unsigned char* alignment, int alignmentLength) { in checkAlignment() argument
599 for (int i = alignmentLength - 1; i >= 0; i--) { in checkAlignment()
636 if (alignmentLength > 0 && alignment[0] == EDLIB_EDOP_INSERT && tIdx >= 0) { in checkAlignment()
649 int getAlignmentStart(const unsigned char* alignment, int alignmentLength, in getAlignmentStart() argument
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/
H A Dprotein.cpp440 alignmentLength = 0; in initialize()
473 alignmentLength = aligned.size(); in setAligned()
477 for(int i=0;i<alignmentLength;i++){ in setAligned()
481 for(int i=alignmentLength-1;i>=0;i--){ in setAligned()
564 return alignmentLength; in getAlignLength()
572 for(int j = 0; j < alignmentLength; j++) { in getStartPos()
623 if (alignmentLength != numBases) { isAligned = true; } in getEndPos()
626 for(int j=alignmentLength-1;j>=0;j--){ in getEndPos()
H A Dsequence.cpp476 alignmentLength = 0; in initialize()
519 alignmentLength = aligned.length(); in setAligned()
523 for(int i=0;i<alignmentLength;i++){ in setAligned()
531 for(int i=alignmentLength-1;i>=0;i--){ in setAligned()
640 return alignmentLength; in getAlignLength()
695 for(int j = 0; j < alignmentLength; j++) { in getStartPos()
750 if (alignmentLength != numBases) { isAligned = true; } in getEndPos()
753 for(int j=alignmentLength-1;j>=0;j--){ in getEndPos()
/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/
H A Dsmithwaterman.cpp234 int alignmentLength = 0; in main() local
247 alignmentLength += len; in main()
253 alignmentLength += len; in main()
269 string gapped_ref = string(reference).substr(referencePos, alignmentLength); in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/
H A Dsmithwaterman.cpp234 int alignmentLength = 0; in main() local
247 alignmentLength += len; in main()
253 alignmentLength += len; in main()
269 string gapped_ref = string(reference).substr(referencePos, alignmentLength); in main()
/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/
H A Dsmithwaterman.cpp234 int alignmentLength = 0; in main() local
247 alignmentLength += len; in main()
253 alignmentLength += len; in main()
269 string gapped_ref = string(reference).substr(referencePos, alignmentLength); in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/unassigned_or_unused/tutorials_custim_io/
H A Dparse_blastn.cpp28 unsigned alignmentLength; member
39 identity(0), alignmentLength(0), mismatches(0), gapOpens(0), in BlastnTabAlignmentRecord()
56 appendNumber(writer, record.alignmentLength); in writeRecord()
127 lexicalCast(record.alignmentLength, buffer); in readRecord()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/util_msa_distance/
H A DMSADistanceAlgorithm.cpp108 : usePercents(true), excludeGaps(false), alignmentLength(0) { in MSADistanceMatrix()
112 : usePercents(_usePercents), excludeGaps(_excludeGaps), alignmentLength(ma->getLength()) { in MSADistanceMatrix()
131 int refSeqLength = excludeGaps ? seqsUngappedLenghts.at(refRow) : alignmentLength; in getSimilarity()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Devaluate_alignment.h281 float alignmentLength = static_cast<float>(length(row(align, 0))); in computeAlignmentStats() local
282 … stats.alignmentSimilarity = 100.0 * static_cast<float>(stats.numPositiveScores) / alignmentLength; in computeAlignmentStats()
283 stats.alignmentIdentity = 100.0 * static_cast<float>(stats.numMatches) / alignmentLength; in computeAlignmentStats()
/dports/biology/edlib/edlib-d5774b4/edlib/include/
H A Dedlib.h212 int alignmentLength; member
269 const unsigned char* alignment, int alignmentLength,

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