/dports/biology/canu/canu-2.2/src/utility/src/utility/ |
H A D | sequence.C | 299 seq[seqLen] = 0; in decode2bitSequence() 388 seq[seqLen] = 0; in decode3bitSequence() 445 seq[seqLen] = 0; in decode8bitSequence() 459 return(seqLen); in encode8bitSequence() 844 seqLen = 0; in loadFASTA() 860 seq[seqLen++] = ch; in loadFASTA() 864 seq[seqLen] = 0; in loadFASTA() 922 seqLen = 0; in loadFASTQ() 967 seq[seqLen] = 0; in loadFASTQ() 1005 seqLen = 0; in loadSequence() [all …]
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H A D | sequence.H | 40 uint32 encode2bitSequence(uint8 *&chunk, char *seq, uint32 seqLen); 41 uint32 encode3bitSequence(uint8 *&chunk, char *seq, uint32 seqLen); 42 uint32 encode8bitSequence(uint8 *&chunk, char *seq, uint32 seqLen); 48 void decode2bitSequence(uint8 *chunk, uint32 chunkLen, char *seq, uint32 seqLen); 49 void decode3bitSequence(uint8 *chunk, uint32 chunkLen, char *seq, uint32 seqLen); 50 void decode8bitSequence(uint8 *chunk, uint32 chunkLen, char *seq, uint32 seqLen); 222 uint8 *&qlt, uint64 &seqMax, uint64 &seqLen, uint32 &errorCode); 238 uint8 *&qlt, uint64 &seqMax, uint64 &seqLen, uint64 &qltLen); 243 uint8 *&qlt, uint64 &seqMax, uint64 &seqLen, uint64 &qltLen);
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/dports/biology/checkm/CheckM-1.0.18/scripts/ |
H A D | simComparePlots.py | 131 genomeId, seqLen, comp, cont = simId.split('-') 155 for seqLen in [20000]: 184 for seqLen in [5000, 20000, 50000]: 207 for seqLen in [5000, 20000, 50000]: 251 seqLens.add(int(seqLen)) 284 for seqLen in [20000]: 360 for seqLen in [5000, 20000, 50000]: 391 for seqLen in [5000, 20000, 50000]: 442 if seqLen != '20000': 453 seqLens.add(int(seqLen)) [all …]
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/dports/devel/duplo/duplo_0.2.0_src/ |
H A D | Duplo.cpp | 115 unsigned int seqLen=0; in process() local 119 seqLen++; in process() 122 reportSeq(y+x-seqLen, x-seqLen, seqLen, pSource1, pSource2, outFile); in process() 125 seqLen=0; in process() 129 if(seqLen >= m_minBlockSize){ in process() 130 reportSeq(m-seqLen, n-seqLen, seqLen, pSource1, pSource2, outFile); in process() 137 unsigned int seqLen=0; in process() local 141 seqLen++; in process() 144 reportSeq(y-seqLen, x+y-seqLen, seqLen, pSource1, pSource2, outFile); in process() 147 seqLen=0; in process() [all …]
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/dports/biology/canu/canu-2.2/src/seqrequester/src/seqrequester/ |
H A D | generate.C | 33 uint64 seqLen = 0; in doGenerate() local 56 seqLen = (uint64)round(len); in doGenerate() 58 if (seqLen+1 >= seqMax) in doGenerate() 59 resizeArrayPair(seq, qlt, 0, seqMax, seqLen+1); in doGenerate() 61 for (uint64 ii=0; ii<seqLen; ii++) { in doGenerate() 82 seq[seqLen] = 0; in doGenerate() 83 qlt[seqLen] = 0; in doGenerate() 85 outputFASTA(stdout, seq, seqLen, 0, genPar.ident, nSeqs); in doGenerate() 88 nBases += seqLen; in doGenerate()
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H A D | summarize.C | 52 seqLen = 0; in doSummarize_loadSequence() 56 resizeArrayPair(seq, qlt, seqLen, seqMax, 2 * (seqLen + bufferLen + 1)); in doSummarize_loadSequence() 61 seqLen += bufferLen; in doSummarize_loadSequence() 63 seq[seqLen] = 0; in doSummarize_loadSequence() 416 if (pos < seqLen) { in doSummarize() 421 if (pos < seqLen) { in doSummarize() 427 while (pos < seqLen) { in doSummarize() 435 ndn += (seqLen < 2) ? 0 : (seqLen-1); in doSummarize() 436 ntn += (seqLen < 3) ? 0 : (seqLen-2); in doSummarize() 442 nBases += seqLen; in doSummarize() [all …]
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H A D | simulate.C | 60 uint64 &seqLen) { in doSimulate_loadSequences() argument 69 seqLen += seq->length(); in doSimulate_loadSequences() 87 uint64 seqLen, // Total length of all sequences in doSimulate_extract() argument 131 sl = seqLen; in doSimulate_extract() 213 uint64 seqLen = 0; in doSimulate() local 215 doSimulate_loadSequences(simPar, seqs, seqLen); in doSimulate() 240 doSimulate_extract(simPar, seqs, seqLen, mt, nReadsMax, nBasesMax); in doSimulate()
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H A D | extract.C | 107 uint64 seqLen = sf->sequenceLength(ss); in doExtract() local 113 if ((seqLen < lmin) || in doExtract() 114 (lmax < seqLen)) in doExtract() 115 seqLen = UINT64_MAX; in doExtract() 118 if (seqLen == UINT64_MAX) in doExtract() 137 bbgn = min(bbgn, seqLen); in doExtract() 138 bend = min(bend, seqLen); in doExtract()
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/ |
H A D | uhmmsearch.cpp | 14 QList<UHMMSearchResult> UHMMSearch::search(plan7_s *_hmm, const char *seq, int seqLen, const UHMMSe… in search() argument 60 …main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nse… in search() 62 …main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &… in search() 165 assert(seqLen > 0); in main_loop_serial() 167 dsq = DigitizeSequence(seq, seqLen); in main_loop_serial() 170 XNU(dsq, seqLen); in main_loop_serial() 178 if (P7ViterbiSpaceOK(seqLen, hmm->M, mx)) { in main_loop_serial() 179 sc = P7Viterbi(dsq, seqLen, hmm, mx, &tr); in main_loop_serial() 181 sc = P7SmallViterbi(dsq, seqLen, hmm, mx, &tr, ti.progress); in main_loop_serial() 188 sc = P7Forward(dsq, seqLen, hmm, NULL); in main_loop_serial() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/util/ |
H A D | masksequence.cpp | 51 unsigned int seqLen = 0; in masksequence() local 52 while (seqData[seqLen] != '\0') { in masksequence() 53 charSequence[seqLen] = (char) subMat->aa2num[static_cast<int>(seqData[seqLen])]; in masksequence() 54 seqLen++; in masksequence() 57 charSequence + seqLen, in masksequence() 67 for (unsigned int pos = 0; pos < seqLen; pos++) { in masksequence() 71 writer.writeData(charSequence, seqLen, reader.getDbKey(id), thread_idx); in masksequence()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/misc/ |
H A D | FindAlgorithm.cpp | 52 if (region.startPos >= seqLen) { in toAnnotation() 123 int seqLen = QByteArray(seq).size(); in getCircularOverlap() local 127 return searchRange.endPos() - seqLen; in getCircularOverlap() 131 int seqLen = QByteArray(seq).size(); in getSearchEndPos() local 156 int seqLen = QByteArray(seq).size(); in findInAmino() local 258 int seqLen = QByteArray(seq).size(); in findInAmino_subst() local 546 if (range.startPos < seqLen && range.endPos() < seqLen) { in findInAmino_regExp() 747 int seqLen, in find() argument 757 Q_UNUSED(seqLen); in find() 761 if (range.endPos() > seqLen) { in find() [all …]
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/dports/biology/checkm/CheckM-1.0.18/checkm/ |
H A D | coverage.py | 40 def __init__(self, seqLen, mappedReads, coverage): argument 41 self.seqLen = seqLen 102 seqIdToSeqLen[seqId] = seqIds[seqId].seqLen 105 for seqId, seqLen in seqIdToSeqLen.iteritems(): 191 for seqId, seqLen in zip(seqIds, seqLens): 202 for read in bamfile.fetch(seqId, 0, seqLen): 228 coverage = float(coverage) / seqLen 269 … coverageInfo[seqId] = CoverageStruct(seqLen=seqLen, mappedReads=numMappedReads, coverage=coverage) 324 seqLen = int(lineSplit[2]) 336 binLength = binStats[binId][bamId][0] + seqLen [all …]
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H A D | coverageWindows.py | 79 def __init__(self, seqLen, mappedReads, coverage): argument 80 self.seqLen = seqLen 177 for seqId, seqLen in zip(seqIds, seqLens): 178 readLoader = ReadLoader(seqLen, bAllReads, minAlignPer, maxEditDistPer) 179 bamfile.fetch(seqId, 0, seqLen, callback=readLoader) 184 while(end < seqLen): 196 coverage = float(sum(readLoader.coverage)) / seqLen 198 queueOut.put((seqId, seqLen, coverage, windowCoverages, readLoader.numReads, 218 …seqId, seqLen, coverage, windowCoverages, numReads, numDuplicates, numSecondary, numFailedQC, numF…
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/dports/biology/edlib/edlib-d5774b4/bindings/python/ |
H A D | performance.py | 17 for seqLen in [30, 100, 1000, 10000, 50000]: 18 query = queryFull[:seqLen] 19 target = targetFull[:seqLen] 20 numRuns = max(1000000000 // (seqLen**2), 1) 22 print('Sequence length: ', seqLen)
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/rna_io/ |
H A D | test_rna_io.h | 60 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 73u); in SEQAN_DEFINE_TEST() 78 record.seqLen = length(record.sequence); in SEQAN_DEFINE_TEST() 121 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 73u); in SEQAN_DEFINE_TEST() 139 record.seqLen = length(record.sequence); in SEQAN_DEFINE_TEST() 176 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 66u); in SEQAN_DEFINE_TEST() 194 record.seqLen = length(record.sequence); in SEQAN_DEFINE_TEST() 230 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 74u); in SEQAN_DEFINE_TEST() 250 record.seqLen = 9u; in SEQAN_DEFINE_TEST() 302 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 50u); in SEQAN_DEFINE_TEST() 362 SEQAN_ASSERT_EQ(rnaRecord.seqLen, 8u); in SEQAN_DEFINE_TEST() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Gui/src/util/ |
H A D | CreateAnnotationFullWidget.cpp | 36 CreateAnnotationFullWidget::CreateAnnotationFullWidget(const qint64 seqLen, QWidget *parent) in CreateAnnotationFullWidget() argument 39 seqLen(seqLen), in CreateAnnotationFullWidget() 159 auto isSimpleSplitLocation = [&location](qint64 seqLen) { in setLocation() argument 163 return location->regions[0].endPos() == seqLen && location->regions[1].startPos == 0; in setLocation() 177 if (location->isMultiRegion() && isSimpleSplitLocation(seqLen)) { in setLocation() 184 isValidLocation = (start >= 1 && start <= seqLen && end >= 1 && end <= seqLen); in setLocation() 198 … (location->regions.size() == 2 && !isSimpleSplitLocation(seqLen)); in setLocation() 284 isValidLocation = (startPos >= 1 && startPos <= seqLen && endPos >= 1 && endPos <= seqLen); in sl_regionChanged() 288 if (startPos <= seqLen && endPos >= 1) { in sl_regionChanged() 289 location->regions << U2Region(startPos - 1, seqLen - startPos + 1); in sl_regionChanged()
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H A D | RangeSelector.cpp | 194 : QDialog(_parent), seqLen(_seqLen), selectedRanges(_regions), isCircular(_isCircular) { in MultipleRangeSelector() 201 ui->startEdit->setValidator(new QIntValidator(1, seqLen, ui->startEdit)); in MultipleRangeSelector() 202 ui->endEdit->setValidator(new QIntValidator(1, seqLen, ui->endEdit)); in MultipleRangeSelector() 204 int w = qMax(((int)log10((double)seqLen)) * 10, 70); in MultipleRangeSelector() 211 ui->endEdit->setText(QString::number(seqLen)); in MultipleRangeSelector() 220 loc = QString("1..%1").arg(seqLen); in MultipleRangeSelector() 255 if (!ok || v1 < 1 || v1 > seqLen) { in accept() 259 if (!ok || (v2 < v1 && !isCircular) || v2 > seqLen) { in accept() 266 …ocation(locEditText.constData(), ui->multipleRegionEdit->text().length(), currentLocation, seqLen); in accept() 318 currentRegions.append(U2Region(st - 1, seqLen - st + 1)); in getSelectedRegions() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/linclust/ |
H A D | KmerIndex.h | 35 unsigned short seqLen; member 44 unsigned short seqLen; member 45 KmerEntry(size_t kmer, unsigned int id, unsigned short pos, unsigned short seqLen) : in KmerEntry() 46 kmer(kmer), id(id), pos(pos), seqLen(seqLen) {} in KmerEntry() 96 …rn KmerEntry(kmer, entries[iteratorPos].id, entries[iteratorPos].pos, entries[iteratorPos].seqLen); in getNextEntry() 140 …ted(const size_t kmer, unsigned int id, unsigned short pos, unsigned short seqLen, bool isReverse){ in addElementSorted() argument 153 entries[writingPosition].seqLen = seqLen; in addElementSorted() 228 Debug(Debug::INFO) << kmer.seqLen << "\t"; in printIndex()
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/dports/biology/ugene/ugene-40.1/src/plugins/circular_view/src/ |
H A D | CircularView.cpp | 97 visibleRange = U2Region(0, seqLen); in mousePressEvent() 571 int seqLen = ctx->getSequenceLength(); in drawSequenceSelection() local 635 float halfChar = 180 / (float)seqLen; in drawRulerNotches() 637 if (currentNotch > seqLen) { in drawRulerNotches() 638 currentNotch = seqLen; in drawRulerNotches() 727 drawRulerNotches(p, startPos, seqLen, seqLen); in drawRulerCoordinates() 732 if (start == seqLen) { in drawRulerCoordinates() 734 } else if (start + span > seqLen) { in drawRulerCoordinates() 735 int span1 = seqLen - start; in drawRulerCoordinates() 784 int seqLen = ctx->getSequenceLength(); in buildAnnotationItem() local [all …]
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/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
H A D | biascorrection.cpp | 238 int seqLen = transcript.length(); in processTranscript() local 240 char seq[seqLen]; in processTranscript() 241 char c_seq[seqLen]; in processTranscript() 247 while (seqLen > lengthBins[lenClass] && lenClass < 4) in processTranscript() 263 for (int i=0; i < seqLen; i++) in processTranscript() 318 _endSeqExp(j,v) += fpkm*(_frag_len_dist->cdf(seqLen-i)); in processTranscript() 340 int seqLen = transcript.length(); in getBias() local 342 char seq[seqLen]; in getBias() 343 char c_seq[seqLen]; in getBias() 349 while (seqLen > lengthBins[lenClass] && lenClass < 4) in getBias() [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/org/gmod/schema/sequence/ |
H A D | Feature.java | 27 private Integer seqLen = -1; field in Feature 198 seqLen = 0; in setResidues() 202 seqLen = residues.length; in setResidues() 213 if (this.seqLen.intValue() == -1 && residues != null) { in getSeqLen() 216 return this.seqLen.intValue(); in getSeqLen() 223 public void setSeqLen(Integer seqLen) { in setSeqLen() argument 224 if (seqLen == null) { in setSeqLen() 227 this.seqLen = seqLen; in setSeqLen()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_align/ |
H A D | graph_align_banded_needleman_wunsch.h | 105 TSize seqLen = 1; in _alignBandedNeedlemanWunschTrace() local 119 --col; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 122 --row; ++col; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 124 --row; ++seqLen; in _alignBandedNeedlemanWunschTrace() 130 --row; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 133 --row; ++col; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 135 --col; ++seqLen; in _alignBandedNeedlemanWunschTrace() 140 --row; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 143 --col; seqLen = 1; in _alignBandedNeedlemanWunschTrace() 145 --row; ++col; ++seqLen; in _alignBandedNeedlemanWunschTrace() [all …]
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/dports/biology/star/STAR-2.7.9a/source/ |
H A D | ClipCR4.cpp | 82 uint32 ClipCR4::polyTail3p(char *seq, uint32 seqLen) in polyTail3p() argument 85 if (seqLen<20) in polyTail3p() 88 uint32_t ib1=seqLen-1; in polyTail3p() 90 for (uint32_t ib=1; ib<=seqLen; ib++) { in polyTail3p() 91 if ( seq[seqLen-ib] == 0 ) {//A-tail in polyTail3p()
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/dports/biology/abyss/abyss-2.3.1/KAligner/ |
H A D | Aligner.cpp | 91 bool isRC, bool good, int read_ind, int seqLen) in alignKmer() argument 113 read_ind, seqLen, m_hashSize); in alignKmer() 117 seqLen, isRC); in alignKmer() 131 int seqLen = seq.length(); in getAlignmentsInternal() local 132 int last_kmer = seqLen - m_hashSize; in getAlignmentsInternal() 138 alignKmer(aligns, seq, isRC, good, 0, seqLen); in getAlignmentsInternal() 144 alignKmer(aligns, seq, isRC, good, last_kmer, seqLen); in getAlignmentsInternal() 148 if (good && seqLen <= 2 * m_hashSize && aligns.size() == 1) { in getAlignmentsInternal() 168 alignKmer(aligns, seq, isRC, good, i, seqLen); in getAlignmentsInternal()
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/dports/biology/checkm/CheckM-1.0.18/checkm/plot/ |
H A D | nxPlot.py | 47 for seqLen in seqLens: 48 testSum += seqLen 51 nx.append(seqLen) 79 for seqLen in yticks: 80 label = '%.1f' % (float(seqLen) / 1000)
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