| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/pairhmm/ |
| H A D | DragstrReadSTRAnalyzer.java | 53 private final int seqLength; field in DragstrReadSTRAnalyzer
55 private DragstrReadSTRAnalyzer(final int seqLength, final int[][] repeatsByPeriodAndPosition, in DragstrReadSTRAnalyzer()
78 final int seqLength = bases.length; in of() local
152 …private static void analyzeBases(final byte[] bases, final int seqLength, final int[][] repeatsByP… in analyzeBases()
181 …atic void calculateRepeatsForPeriodTwoAndAbove(final byte[] bases, final int seqLength, final int … in calculateRepeatsForPeriodTwoAndAbove()
337 …private static void calculateRepeatsForPeriodOne(final byte[] bases, final int seqLength, final in… in calculateRepeatsForPeriodOne()
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| /dports/biology/canu/canu-2.2/src/meryl/src/meryl/ |
| H A D | merylInput.C | 245 uint64 &seqLength, in loadBasesFromCanu()
255 uint64 &seqLength, in loadBasesFromCanu()
311 uint64 &seqLength, in loadBases()
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| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | suffixtree.cpp | 56 int seqLength = sequence.length(); // make it a cononical suffix tree in loadSequence() local
89 int seqLength = compareSequence.length(); // time complexity should be O(L) in countSuffixes() local
133 int seqLength = compareSequence.length(); // time complexity should be O(L) in countSuffixes() local
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| H A D | qualityscores.h | 62 int seqLength; variable
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| H A D | qualityscores.cpp | 413 int seqLength = sequence.getNumBases(); in stripQualThreshold() local
448 int seqLength = sequence.getNumBases(); in stripQualRollingAverage() local
499 int seqLength = sequence.getNumBases(); in stripQualWindowAverage() local
613 int seqLength = errorSeq.size(); in updateQScoreErrorMap() local
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| /dports/math/mlpack/mlpack-3.4.2/src/mlpack/methods/ann/layer/ |
| H A D | lookup_impl.hpp | 37 const size_t seqLength = input.n_rows; in Forward() local
69 const size_t seqLength = input.n_rows; in Gradient() local
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/ |
| H A D | EvalueComputation.h | 32 double area(double score, double seqLength){ in area()
36 inline double computeEvalue(double score, double seqLength) { in computeEvalue()
42 inline double computeLogEvalue(double score, double seqLength) { in computeLogEvalue()
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| /dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/ |
| H A D | GenomeAlignerIndexTask.cpp | 60 SAType getPartStartPos(SAType seqLength, int parts, int curPart) { in getPartStartPos()
68 SAType getPartLength(SAType seqLength, int parts, int curPart) { in getPartLength()
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| H A D | GenomeAlignerSearchQuery.h | 91 quint32 seqLength; variable
|
| /dports/biology/bedtools/bedtools2-2.30.0/src/nucBed/ |
| H A D | nucBed.cpp | 40 void NucBed::ReportDnaProfile(const BED& bed, const string &sequence, CHRPOS seqLength) in ReportDnaProfile()
128 CHRPOS seqLength = fr.sequenceLength(bed.chrom); in ProfileDNA() local
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/indexed_fasta_io/ |
| H A D | base.cpp | 47 unsigned seqLength = sequenceLength(faiIndex, idx); in main() local
|
| /dports/misc/py-mxnet/incubator-mxnet-1.9.0/scala-package/examples/src/main/scala/org/apache/mxnetexamples/rnn/ |
| H A D | TestCharRnn.scala | 63 val seqLength = 1200 constant
146 val seqLength = 1200 constant
|
| /dports/misc/mxnet/incubator-mxnet-1.9.0/scala-package/examples/src/main/scala/org/apache/mxnetexamples/rnn/ |
| H A D | TestCharRnn.scala | 63 val seqLength = 1200 constant
146 val seqLength = 1200 constant
|
| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/ |
| H A D | SamQuerySeqWithRefHelper.cpp | 252 int32_t seqLength = updatedSeq.length(); in seqWithEquals() local
305 int32_t seqLength = updatedSeq.length(); in seqWithoutEquals() local
|
| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/misc/ |
| H A D | SequenceContentFilterTask.cpp | 76 const qint64 seqLength = seqObject->getSequenceLength(); in sequenceContainsPattern() local
107 const qint64 seqLength = seqObject->getSequenceLength(); in searchThroughRegion() local
|
| /dports/biology/seqan1/seqan-1.3.1/apps/seqcons/ |
| H A D | read_simulator.R | 33 seqLength = 100000 # Source sequence length globalVar
85 if (keyvalue[1] == "seqLength") seqLength = as.integer(keyvalue[2]) globalVar
112 createRandomSequence=function(alphabet = c('A','C','G','T'), seqLength = 100, p = rep(1/length(alph… argument
119 createRandomSequenceWithRepeats=function(alphabet = c('A','C','G','T'), seqLength = 100, numOfRepea… argument
148 seqLength = length(seqPoly) functionVar
217 seqLength = length(sourceSeq) functionVar
357 seqLength = length(sourceSeq) functionVar
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| /dports/biology/seqan1/seqan-1.3.1/demos/tutorial/ |
| H A D | find_motif.cpp | 24 TSize seqLength = length(dataset[0]); // length of sequences in main() local
|
| /dports/biology/bamtools/bamtools-2.5.2/src/utils/ |
| H A D | bamtools_fasta.cpp | 86 int seqLength = std::strlen(sequence); in Chomp() local
467 const int seqLength = (stop - start) + 1; in GetSequence() local
499 const int seqLength = (stop - start) + 1; in GetSequence() local
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | consensusseqscommand.h | 46 int seqLength; variable
|
| /dports/misc/mnn/MNN-1.2.0/source/shape/ |
| H A D | ShapeLSTM.cpp | 40 auto seqLength = X->length(0); in onComputeSize() local
|
| /dports/biology/bbmap/bbmap/current/fun/ |
| H A D | ProbShared.java | 16 static int cardinality(int k, int seqLength){ in cardinality()
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| /dports/biology/ugene/ugene-40.1/src/plugins/dna_flexibility/src/ |
| H A D | FindHighFlexRegionsAlgorithm.cpp | 34 const int seqLength, in find()
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| /dports/biology/pbbam/pbbam-0.18.0/src/ |
| H A D | AlignmentPrinter.cpp | 36 int seqLength = 0; in Print() local
|
| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_sequence/sequence_info/ |
| H A D | DinuclOccurTask.cpp | 63 qint64 seqLength = sequenceDbi->getSequenceObject(seqRef.entityId, os).length; in run() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/testutils/ |
| H A D | ReadTestUtils.java | 74 final int seqLength = rdn.nextInt(maxLength - minLength) + minLength; in randomErrorFreeUnpairedReads() local
|