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/dports/biology/canu/canu-2.2/src/utility/src/utility/
H A Dsequence.C299 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 …]
H A Dsequence.H40 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);
/dports/biology/checkm/CheckM-1.0.18/scripts/
H A DsimComparePlots.py131 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))
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/dports/devel/duplo/duplo_0.2.0_src/
H A DDuplo.cpp115 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 …]
/dports/biology/canu/canu-2.2/src/seqrequester/src/seqrequester/
H A Dgenerate.C33 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()
H A Dsummarize.C52 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 …]
H A Dsimulate.C60 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()
H A Dextract.C107 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()
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/
H A Duhmmsearch.cpp14 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()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/util/
H A Dmasksequence.cpp51 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()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/misc/
H A DFindAlgorithm.cpp52 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()
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/dports/biology/checkm/CheckM-1.0.18/checkm/
H A Dcoverage.py40 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
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H A DcoverageWindows.py79 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…
/dports/biology/edlib/edlib-d5774b4/bindings/python/
H A Dperformance.py17 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)
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/rna_io/
H A Dtest_rna_io.h60 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 …]
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Gui/src/util/
H A DCreateAnnotationFullWidget.cpp36 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()
H A DRangeSelector.cpp194 : 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 …]
/dports/biology/mmseqs2/MMseqs2-13-45111/src/linclust/
H A DKmerIndex.h35 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()
/dports/biology/ugene/ugene-40.1/src/plugins/circular_view/src/
H A DCircularView.cpp97 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 …]
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/
H A Dbiascorrection.cpp238 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 …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/org/gmod/schema/sequence/
H A DFeature.java27 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/graph_align/
H A Dgraph_align_banded_needleman_wunsch.h105 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 …]
/dports/biology/star/STAR-2.7.9a/source/
H A DClipCR4.cpp82 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()
/dports/biology/abyss/abyss-2.3.1/KAligner/
H A DAligner.cpp91 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()
/dports/biology/checkm/CheckM-1.0.18/checkm/plot/
H A DnxPlot.py47 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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