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Searched refs:numBases (Results 1 – 25 of 173) sorted by relevance

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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A DseqIOALF.c348 int numBases; /* number of nucleotides read in */ in fread_alf() local
356 && numBases<BASELIMIT;) { in fread_alf()
380 read->base[numBases] = ch; in fread_alf()
381 read->prob_A[numBases] = 0; in fread_alf()
382 read->prob_C[numBases] = 0; in fread_alf()
383 read->prob_G[numBases] = 0; in fread_alf()
384 read->prob_T[numBases] = 0; in fread_alf()
385 read->basePos[numBases] = bp; in fread_alf()
386 ++numBases; in fread_alf()
389 read->base[numBases] = 0; in fread_alf()
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/dports/biology/bamutil/bamUtil-1.0.15/src/
H A DReadReference.cpp60 int numBases = UNSPECIFIED_INT; in execute() local
71 LONG_INTPARAMETER("numBases", &numBases) in execute()
83 ((end == UNSPECIFIED_INT) && (numBases == UNSPECIFIED_INT))) in execute()
90 if((end != UNSPECIFIED_INT) && (numBases != UNSPECIFIED_INT)) in execute()
97 else if(numBases != UNSPECIFIED_INT) in execute()
99 end = start + numBases; in execute()
/dports/biology/mothur/mothur-1.46.1/source/datastructures/
H A Dsffread.cpp75 numBases = be_int4(*(unsigned int *)(readNumBases)); in readSff()
135 flowIndex.resize(numBases); in readSff()
136 char* flowI = new char[numBases]; in readSff()
138 for (int i = 0; i < numBases; i++) { in readSff()
147 char* readBases = new char[numBases]; in readSff()
148 in.read(&(*readBases), numBases); in readSff()
153 qualScores.resize(numBases, 0); in readSff()
154 char* scores = new char[numBases]; in readSff()
156 for (int i = 0; i < numBases; i++) { in readSff()
284 out.write(entireRead[11], numBases); //write bases in printSff()
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H A Dsequence.cpp71 …if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the… in Sequence()
475 numBases = 0; in initialize()
505 numBases = unaligned.length(); in setUnaligned()
605 return numBases; in getNumBases()
648 for(int j=0;j<numBases;j++){ in getAmbigBases()
676 for(int j=1;j<numBases;j++){ in getLongHomoPolymer()
750 if (alignmentLength != numBases) { isAligned = true; } in getEndPos()
760 if(!isAligned){ endPos = numBases; } in getEndPos()
795 for(int i=numBases-1;i>=0;i--){ in reverseComplement()
811 if(numBases > length){ in trim()
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H A Dsffread.hpp84 unsigned int getNumBases() { return numBases; } in getNumBases()
102 void setNumBases(unsigned int n) { numBases = n; } in setNumBases()
117 unsigned int numBases; member in SffRead
H A Dprotein.cpp439 numBases = 0; in initialize()
461 numBases = unaligned.size(); in setUnaligned()
539 int Protein::getNumBases(){ return numBases; } in getNumBases()
623 if (alignmentLength != numBases) { isAligned = true; } in getEndPos()
633 if(!isAligned){ endPos = numBases; } in getEndPos()
666 if(numBases > length){ in trim()
668 numBases = length; in trim()
H A Doptiblastmatrix.cpp61 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq; in readBlast() local
76 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in readBlast()
80 lengthThisSeq = numBases; in readBlast()
114 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in readBlast()
185 lengthThisSeq = numBases; in readBlast()
290 …in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuer… in readBlast()
294 lengthThisSeq = numBases; in readBlast()
340 …in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuer… in readBlast()
424 lengthThisSeq = numBases; in readBlast()
H A Doptidb.cpp21 numBases = baseMap.size(); //A,T,G,C,-,N in OptiDB()
45 thisDistribution.resize(numBases); in get()
253 counts.resize(numBases, 0.0); in calcIndicatorColumns()
H A Doptidb.hpp42 int alignedLength, numBases; member in OptiDB
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dabiview.c101 ajlong numBases; in main() local
142 numBases = ajSeqABIGetNBase(fp); in main()
148 numBases = base_end; in main()
150 if(numBases < base_start) in main()
152 base_start,numBases); in main()
156 window = (ajint) numBases+1; /* Lossy cast */ in main()
182 ajSeqABIReadSeq(fp,baseO,numBases,&nseq); in main()
225 while(nstart < numBases-1) in main()
227 if(nstop > numBases) in main()
228 nstop = (ajint) numBases; /* Lossy cast */ in main()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/
H A DABIFormat.cpp473 uint numPoints, numBases; in loadABIObjects() local
509 numBases = 0; in loadABIObjects()
517 cd.prob_A.resize(numBases + 1); in loadABIObjects()
518 cd.prob_C.resize(numBases + 1); in loadABIObjects()
519 cd.prob_G.resize(numBases + 1); in loadABIObjects()
520 cd.prob_T.resize(numBases + 1); in loadABIObjects()
521 cd.baseCalls.resize(numBases + 1); in loadABIObjects()
602 QVector<uchar> conf(numBases); in loadABIObjects()
615 QByteArray qualCodes(numBases, 0); in loadABIObjects()
747 if (numBases > 1) { in loadABIObjects()
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/dports/biology/clustalw/clustalw-2.1/src/alignment/
H A DSequence.cpp193 int c, numResidues, numBases; in checkDNAFlag() local
197 numResidues = numBases = 0; in checkDNAFlag()
208 numBases++; in checkDNAFlag()
215 numBases++; in checkDNAFlag()
222 if ((numBases == 0) || (numResidues == 0)) in checkDNAFlag()
226 ratio = (float)numBases / (float)numResidues; in checkDNAFlag()
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/
H A Dajseqabi.c121 AjBool ajSeqABIReadConfid(AjPFile fp,ajlong pconO,ajlong numBases, in ajSeqABIReadConfid() argument
131 for (i=0;i<(ajint)numBases;i++) in ajSeqABIReadConfid()
157 AjBool ajSeqABIReadSeq(AjPFile fp,ajlong baseO,ajlong numBases, in ajSeqABIReadSeq() argument
163 ajDebug("ajSeqABIReadSeq base0 %Ld numBases %Ld\n", baseO, numBases); in ajSeqABIReadSeq()
167 for (i=0;i<(ajint)numBases;i++) in ajSeqABIReadSeq()
265 ajlong numBases; in ajSeqABIGetNBase() local
271 if(!seqABIGetFlag(fp,BASEtag,2,3,&numBases)) in ajSeqABIGetNBase()
272 if(!seqABIGetFlag(fp,BASEtag,1,3,&numBases)) in ajSeqABIGetNBase()
278 return (ajint) numBases; in ajSeqABIGetNBase()
337 void ajSeqABIGetBasePosition(AjPFile fp,ajlong numBases, in ajSeqABIGetBasePosition() argument
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H A Dajseqabi.h73 void ajSeqABIGetBasePosition(AjPFile fp,ajlong numBases,
90 AjBool ajSeqABIReadConfid(AjPFile fp,ajlong pconO,ajlong numBases,
92 AjBool ajSeqABIReadSeq(AjPFile fp,ajlong baseO,ajlong numBases,
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/fx_tools/
H A Dfx_fastq_stats.cpp83 seqan::String<int64_t> numBases; member
132 resize(numBases, n, 0); in resizeToReadLength()
158 numBases[i] += 1; in registerRead()
166 if (numBases[i] == 0u || minScores[i] > qual) in registerRead()
168 if (numBases[i] == 0u || maxScores[i] < qual) in registerRead()
180 meanScores[i] = (1.0 * sumScores[i]) / numBases[i]; in finalizeStats()
188 unsigned n = numBases[i]; // Number of bases. in finalizeStats()
331 << stats.numBases[i] << "\t" in main()
/dports/biology/checkm/CheckM-1.0.18/checkm/
H A DbinUnion.py50 def numBases(self): member in UnionBin
138 fiftyPercent = 0.5 * current.numBases()
142 fiftyPercentBest = 0.5 * bestBin.numBases()
163 … bestBin.numBases(),
164 … current.numBases(),
/dports/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/
H A DAssembly.pm378 $self->{totalbp} = defined $all->{numBases} ? $all->{numBases} : 0;
379 $self->{totalbp1k} = defined $large->{numBases} ? $large->{numBases} : 0;
446 $out{numBases} = $avglen;
/dports/biology/mothur/mothur-1.46.1/source/calculators/
H A Dkimura.cpp15 int numBases = A.getAlignLength(); in calcDist() local
21 for (int i = 0; i < numBases; i++) { in calcDist()
/dports/biology/bbmap/bbmap/current/dna/
H A DMotifMulti.java57 public int numBases() { in numBases() method in MotifMulti
58 return sub[0].numBases(); in numBases()
/dports/biology/mothur/mothur-1.46.1/source/read/
H A Dreadblast.cpp49 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq; in read() local
67 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in read()
71 lengthThisSeq = numBases; in read()
102 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in read()
175 lengthThisSeq = numBases; in read()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/
H A Dalnvec.cpp558 void CAlnVec::CollectNucleotideFrequences(const string& col, int base_count[], int numBases) in CollectNucleotideFrequences() argument
562 fill_n(base_count, numBases, 0); in CollectNucleotideFrequences()
636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences() argument
640 fill_n(base_count, numBases, 0); in CollectProteinFrequences()
646 if (0<=pos && pos < numBases) in CollectProteinFrequences()
655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local
698 CollectNucleotideFrequences(segs[i], base_count, numBases); in CreateConsensus()
700 CollectProteinFrequences(segs[i], base_count, numBases); in CreateConsensus()
711 for (int k = 0; k < numBases; ++k) { in CreateConsensus()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/
H A Dalnvec.cpp558 void CAlnVec::CollectNucleotideFrequences(const string& col, int base_count[], int numBases) in CollectNucleotideFrequences() argument
562 fill_n(base_count, numBases, 0); in CollectNucleotideFrequences()
636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences() argument
640 fill_n(base_count, numBases, 0); in CollectProteinFrequences()
646 if (0<=pos && pos < numBases) in CollectProteinFrequences()
655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local
698 CollectNucleotideFrequences(segs[i], base_count, numBases); in CreateConsensus()
700 CollectProteinFrequences(segs[i], base_count, numBases); in CreateConsensus()
711 for (int k = 0; k < numBases; ++k) { in CreateConsensus()
/dports/biology/mothur/mothur-1.46.1/source/chimera/
H A Dmaligner.cpp158 int numBases = 0; in minCoverageFilter() local
165 numBases++; in minCoverageFilter()
173 int coverage = ((numCovered/(float)numBases)*100); in minCoverageFilter()
545 float numBases = (countA + countB) /(float) 2; in computePercentID() local
547 if (numBases == 0) { return 0; } in computePercentID()
549 float percentIdentical = (numIdentical/(float)numBases) * 100; in computePercentID()
/dports/games/osgg/Osgg-32d9e02/
H A Dserver.cpp108 int numBases; // Number of bases on map, set by loadMap member
296 gameInfo.numBases=0; in loadMap()
385 gameInfo.numBases++; in loadMap()
393 if(te.type==entBase && te.id != gameInfo.numBases) in loadMap()
395 …cout << "error: base entity have id:" << te.id << " but numBases is:" << gameInfo.numBases << endl; in loadMap()
933 if(gameInfo.numBases > 1) in main()
/dports/java/bouncycastle15/crypto-169/core/src/test/java/org/bouncycastle/math/test/
H A DPrimesTest.java158 private static boolean referenceIsMRProbablePrime(BigInteger x, int numBases)
162 for (int i = 0; i < numBases; ++i)

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