/dports/biology/sra-tools/sra-tools-2.11.0/tools2/assemble-fragments/ |
H A D | fragment.hpp | 324 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 [all …]
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H A D | generate-test-data.pl | 117 …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", $_), readNo => 2, sequence => sequence(10000 + ($_ - …
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H A D | filter-ir.cpp | 51 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()
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H A D | assemble-fragments.cpp | 98 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()
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H A D | sam2ir.cpp | 49 int32_t const readNo = (flags >> 6) & 3; in writeRow() local 61 out.value(3, readNo); in writeRow()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
H A D | outputFormat.h | 291 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 [all …]
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H A D | razers.h | 843 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; [all …]
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H A D | razers_matepairs.h | 542 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;
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/dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
H A D | outputFormat.h | 289 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() [all …]
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H A D | razers.h | 831 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; [all …]
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H A D | razers_spliced.h | 190 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() [all …]
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H A D | razers_matepairs.h | 575 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;
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | outputFormat.h | 332 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() [all …]
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H A D | razers.h | 875 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) [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
H A D | outputFormat.h | 295 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() [all …]
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H A D | razers.h | 864 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; [all …]
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H A D | razers_matepairs.h | 250 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;
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H A D | razers_spliced.h | 190 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
H A D | outputFormat.h | 289 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() [all …]
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H A D | razers.h | 852 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; [all …]
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H A D | razers_matepairs.h | 554 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;
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/fastq-loader/ |
H A D | common-writer.c | 257 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() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/util/ |
H A D | pseudo-aligner.cpp | 313 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
H A D | loader-imp.c | 143 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() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
H A D | razers.h | 1532 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) [all …]
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