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Searched refs:readNo (Results 1 – 25 of 35) sorted by relevance

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/dports/biology/sra-tools/sra-tools-2.11.0/tools2/assemble-fragments/
H A Dfragment.hpp324 int readNo; member
329 Alignment(int readNo, std::string const &sequence) in Alignment()
330 : readNo(readNo) in Alignment()
338 : readNo(readNo) in Alignment()
352 return Alignment(readNo, ""); in truncated()
356 if (a.readNo < b.readNo) in operator <()
409 DNASequence const &sequence(int readNo) const { in sequence()
413 if (i.readNo != readNo) continue; in sequence()
422 if (detail[i].readNo != readNo) continue; in sequence()
461 auto const readNo = in.read(r, 3).value<int32_t>(); in read() local
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H A Dgenerate-test-data.pl117 …push @contig, { name => sprintf("SPOT_%02u", $_), readNo => 1, sequence => sequence(10000 + ($_ - …
118 …push @contig, { name => sprintf("SPOT_%02u", $_), readNo => 2, sequence => sequence(10425 + ($_ - …
121 …push @contig, { name => sprintf("SPOT_%02u", $_), readNo => 1, sequence => sequence(10425 + ($_ - …
122 …push @contig, { name => sprintf("SPOT_%02u", $_), readNo => 2, sequence => sequence(10000 + ($_ - …
H A Dfilter-ir.cpp51 out.value(3 + (table - 1) * 8, int32_t(i.readNo)); in write()
85 auto const readNo = fragment.detail[first].readNo; in shouldKeep() local
87 while (next < n && fragment.detail[next].readNo == readNo) in shouldKeep()
H A Dassemble-fragments.cpp98 double pileUpDepth(int readNo) const { in pileUpDepth()
100 auto const start = readNo == 1 ? start1 : start2; in pileUpDepth()
101 auto const end = readNo == 1 ? end1 : end2; in pileUpDepth()
102 auto const avglen = readNo == 1 ? qlength1.average() : qlength2.average(); in pileUpDepth()
363 if (one->readNo != 1 || one->aligned == false) continue; in candidateFragmentAlignments()
372 if (two->readNo != 2 || two->aligned == false) continue; in candidateFragmentAlignments()
648 …auto const layout = std::to_string(first.readNo) + first.strand + std::to_string(second.readNo) + … in assemble()
650 …auto const sequence = fragment.sequence(first.readNo) + fragment.sequence(second.readNo); ///< jus… in assemble()
695 badReadNo.setValue(i.readNo); in assemble()
H A Dsam2ir.cpp49 int32_t const readNo = (flags >> 6) & 3; in writeRow() local
61 out.value(3, readNo); in writeRow()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/
H A DoutputFormat.h291 unsigned readNo = -1; in countCoocurrences() local
308 readNo = (*it).rseqNo; in countCoocurrences()
497 unsigned readNo = -1; in assignMappingQuality() local
512 readNo = (*it).rseqNo; in assignMappingQuality()
639 unsigned readNo = 0; in dumpUnmappedReads() local
654 ++readNo; in dumpUnmappedReads()
660 ++readNo; in dumpUnmappedReads()
667 file << headerChar << readIDs[readNo] << std::endl << reads[readNo] << std::endl; in dumpUnmappedReads()
675 ++readNo; in dumpUnmappedReads()
1038 for(unsigned readNo = 0; readNo < length(reads); ++readNo) in dumpMatches() local
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H A Drazers.h843 unsigned readNo = -1;
860 readNo = (*it).rseqNo;
892 readNo = (*it).rseqNo;
917 unsigned readNo = -1;
931 readNo = (*it).rseqNo;
996 unsigned readNo = -1;
1057 readNo = (*it).rseqNo;
1093 unsigned readNo = -1;
1132 readNo = (*it).rseqNo;
1165 unsigned readNo = -1;
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H A Drazers_matepairs.h542 unsigned readNo = -1;
558 if (readNo == ((*it).rseqNo >> 1))
571 setMaxErrors(swiftL, readNo, maxErrors);
572 setMaxErrors(swiftR, readNo, maxErrors);
575 ::std::cerr << "(read #" << readNo << " disabled)";
586 readNo = (*it).rseqNo >> 1;
/dports/biology/seqan1/seqan-1.3.1/apps/razers/
H A DoutputFormat.h289 unsigned readNo = -1; in countCoocurrences() local
296 if ((*it).rseqNo == readNo) in countCoocurrences()
306 readNo = (*it).rseqNo; in countCoocurrences()
422 unsigned readNo = -1; in assignMappingQuality() local
437 readNo = (*it).rseqNo; in assignMappingQuality()
440 if(++it!=itEnd && (*it).rseqNo==readNo) in assignMappingQuality()
445 secondBestMatches = cnts[1][readNo] >> 5; in assignMappingQuality()
854 for(unsigned readNo = 0; readNo < length(reads); ++readNo) in dumpMatches() local
872 if (!empty(reads[readNo])) in dumpMatches()
882 file << reads[readNo] << _sep_; in dumpMatches()
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H A Drazers.h831 unsigned readNo = -1;
848 readNo = (*it).rseqNo;
880 readNo = (*it).rseqNo;
905 unsigned readNo = -1;
919 readNo = (*it).rseqNo;
984 unsigned readNo = -1;
1045 readNo = (*it).rseqNo;
1081 unsigned readNo = -1;
1120 readNo = (*it).rseqNo;
1153 unsigned readNo = -1;
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H A Drazers_spliced.h190 unsigned readNo = -1; in compactSplicedMatches() local
208 if (readNo == (*it).rseqNo) in compactSplicedMatches()
225 setMaxErrors(swiftL, readNo, maxErrors); in compactSplicedMatches()
249 readNo = (*it).rseqNo;// >> 1; in compactSplicedMatches()
271 unsigned readNo = -1; in compactSplicedMatchesPurgeAmbiguous() local
289 if (readNo == (*it).rseqNo) in compactSplicedMatchesPurgeAmbiguous()
306 readNo = (*it).rseqNo; in compactSplicedMatchesPurgeAmbiguous()
355 unsigned readNo = -1; in countSplitMatches() local
363 if (readNo == (*it).rseqNo && in countSplitMatches()
370 readNo = (*it).rseqNo; in countSplitMatches()
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H A Drazers_matepairs.h575 unsigned readNo = -1;
591 if (readNo == ((*it).rseqNo >> 1))
604 setMaxErrors(swiftL, readNo, maxErrors);
605 setMaxErrors(swiftR, readNo, maxErrors);
608 ::std::cerr << "(read #" << readNo << " disabled)";
619 readNo = (*it).rseqNo >> 1;
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A DoutputFormat.h332 unsigned readNo = -1; in countCoocurrences() local
339 if ((*it).readId == readNo) in countCoocurrences()
349 readNo = (*it).readId; in countCoocurrences()
450 unsigned readNo = -1; in assignMappingQuality() local
465 readNo = (*it).readId; in assignMappingQuality()
468 if(++it!=itEnd && (*it).readId==readNo) in assignMappingQuality()
473 secondBestMatches = cnts[1][readNo] >> 5; in assignMappingQuality()
855 for(unsigned readNo = 0; readNo < length(store.readSeqStore); ++readNo) in dumpMatches() local
874 if (it == itEnd || readNo < (*it).readId) in dumpMatches()
876 if (!empty(store.readSeqStore[readNo])) in dumpMatches()
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H A Drazers.h875 int minT = _qgramLemma(swift, readNo, maxErrors);
880 setMinThreshold(swift, readNo, (unsigned)minT);
917 unsigned readNo = -1;
952 setMaxErrors(swift, readNo, maxErrors);
974 readNo = (*it).readId;
1005 unsigned readNo = -1;
1016 if (readNo == (*it).readId)
1044 readNo = (*it).readId;
1077 unsigned readNo = -1;
1090 if (readNo == (*it).readId)
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/
H A DoutputFormat.h295 unsigned readNo = -1; in countCoocurrences() local
302 if ((*it).rseqNo == readNo) in countCoocurrences()
312 readNo = (*it).rseqNo; in countCoocurrences()
428 unsigned readNo = -1; in assignMappingQuality() local
443 readNo = (*it).rseqNo; in assignMappingQuality()
446 if(++it!=itEnd && (*it).rseqNo==readNo) in assignMappingQuality()
451 secondBestMatches = cnts[1][readNo] >> 5; in assignMappingQuality()
860 for(unsigned readNo = 0; readNo < length(reads); ++readNo) in dumpMatches() local
878 if (!empty(reads[readNo])) in dumpMatches()
888 file << reads[readNo] << _sep_; in dumpMatches()
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H A Drazers.h864 unsigned readNo = -1;
883 readNo = (*it).rseqNo;
916 readNo = (*it).rseqNo;
945 unsigned readNo = -1;
959 readNo = (*it).rseqNo;
1026 unsigned readNo = -1;
1089 readNo = (*it).rseqNo;
1131 unsigned readNo = -1;
1170 readNo = (*it).rseqNo;
1204 unsigned readNo = -1;
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H A Drazers_matepairs.h250 unsigned readNo = -1;
269 if (readNo == ((*it).rseqNo >> 1))
282 setMaxErrors(swiftL, readNo, maxErrors);
283 setMaxErrors(swiftR, readNo, maxErrors);
286 ::std::cerr << "(read #" << readNo << " disabled)";
309 readNo = (*it).rseqNo >> 1;
H A Drazers_spliced.h190 unsigned readNo = -1; in compactSplicedMatches() local
208 if (readNo == (*it).rseqNo) in compactSplicedMatches()
225 setMaxErrors(swiftL, readNo, maxErrors); in compactSplicedMatches()
249 readNo = (*it).rseqNo;// >> 1; in compactSplicedMatches()
271 unsigned readNo = -1; in compactSplicedMatchesPurgeAmbiguous() local
289 if (readNo == (*it).rseqNo) in compactSplicedMatchesPurgeAmbiguous()
306 readNo = (*it).rseqNo; in compactSplicedMatchesPurgeAmbiguous()
355 unsigned readNo = -1; in countSplitMatches() local
363 if (readNo == (*it).rseqNo && in countSplitMatches()
370 readNo = (*it).rseqNo; in countSplitMatches()
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/
H A DoutputFormat.h289 unsigned readNo = -1; in countCoocurrences() local
296 if ((*it).rseqNo == readNo) in countCoocurrences()
306 readNo = (*it).rseqNo; in countCoocurrences()
495 unsigned readNo = -1; in assignMappingQuality() local
510 readNo = (*it).rseqNo; in assignMappingQuality()
513 if(++it!=itEnd && (*it).rseqNo==readNo) in assignMappingQuality()
518 secondBestMatches = cnts[1][readNo] >> 5; in assignMappingQuality()
958 for(unsigned readNo = 0; readNo < length(reads); ++readNo) in dumpMatches() local
976 if (!empty(reads[readNo])) in dumpMatches()
986 file << reads[readNo] << _sep_; in dumpMatches()
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H A Drazers.h852 unsigned readNo = -1;
869 readNo = (*it).rseqNo;
901 readNo = (*it).rseqNo;
926 unsigned readNo = -1;
940 readNo = (*it).rseqNo;
1005 unsigned readNo = -1;
1066 readNo = (*it).rseqNo;
1102 unsigned readNo = -1;
1141 readNo = (*it).rseqNo;
1174 unsigned readNo = -1;
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H A Drazers_matepairs.h554 unsigned readNo = -1;
570 if (readNo == ((*it).rseqNo >> 1))
583 setMaxErrors(swiftL, readNo, maxErrors);
584 setMaxErrors(swiftR, readNo, maxErrors);
587 ::std::cerr << "(read #" << readNo << " disabled)";
598 readNo = (*it).rseqNo >> 1;
/dports/biology/sra-tools/sra-tools-2.11.0/tools/fastq-loader/
H A Dcommon-writer.c257 unsigned readNo; member
334 unsigned readNo = 0; in readSequence() local
415 readNo |= 1; in readSequence()
417 readNo |= 2; in readSequence()
418 if (readNo == 1 || readNo == 2) in readSequence()
422 readNo = 1; in readSequence()
450 rslt->u.sequence.readNo = readNo; in readSequence()
785 unsigned const readNo = rr.u.sequence.readNo; in ArchiveFile() local
852 fi.otherReadNo = readNo; in ArchiveFile()
948 if (readNo != fip->otherReadNo) { in ArchiveFile()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/util/
H A Dpseudo-aligner.cpp313 static void print1FastQ(uint64_t serialNo, int readNo, Sequence const &SEQ, Quality const &QUAL) in print1FastQ() argument
317 out << '@' << serialNo << '/' << readNo << endl; in print1FastQ()
342 static void printSAM(ostream &out, uint64_t name, int readNo, bool reversed, bool secondary, int po… in printSAM() argument
344 …x1 | 0x2 | (reversed ? 0x10 : 0) | (reversed ? 0 : 0x20) | (readNo == 1 ? 0x40 : 0) | (readNo == 2… in printSAM()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/
H A Dloader-imp.c143 uint8_t readNo; member
1689 unsigned readNo = 0; in ProcessBAM() local
1743 readNo |= 1; in ProcessBAM()
1745 readNo |= 2; in ProcessBAM()
1746 switch (readNo) { in ProcessBAM()
1768 readNo = 1; in ProcessBAM()
2104 switch (readNo) { in ProcessBAM()
2224 switch (readNo) { in ProcessBAM()
2297 fi.readNo = readNo; in ProcessBAM()
2378 if (readNo == fip->readNo) { in ProcessBAM()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A Drazers.h1532 int minT = _qgramLemma(filterPattern, readNo, maxErrors);
1568 unsigned readNo = -1;
1628 options.errorCutOff[readNo] = -scoreCutOff;
1631 while (it != itEnd && readNo == (*it).readId)
1646 options.errorCutOff[readNo] = 0;
1648 setMaxErrors(swift, readNo, -1);
1659 options.errorCutOff[readNo] = errors;
1687 readNo = (*it).readId;
1732 unsigned readNo = -1;
1756 if (readNo == (*it).readId)
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