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Searched refs:TContigPos (Results 1 – 25 of 65) sorted by relevance

123

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/
H A Dstore_align_intervals.h124 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in extractAlignIntervals() typedef
135 TContigPos beginPos = align.beginPos; in extractAlignIntervals()
136 TContigPos endPos = align.endPos; in extractAlignIntervals()
139 TContigPos help = beginPos; in extractAlignIntervals()
156 …TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos; // seqPos from Read projected to pos… in extractAlignIntervals()
171 TContigPos seqPos1 = 0; in extractAlignIntervals()
172 TContigPos gapPos1 = 0; in extractAlignIntervals()
173 TContigPos seqPos2 = firstSeqPos; in extractAlignIntervals()
174 TContigPos gapPos2 = firstGapPos; in extractAlignIntervals()
240 TContigPos lastGapPosBeforeGap1; in extractAlignIntervals()
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H A Dstore_all.h1561 typedef typename TFragmentStore::TContigPos TContigPos;
1683 typedef typename TFragmentStore::TContigPos TContigPos;
1748 TContigPos left = align.beginPos;
1749 TContigPos right = align.endPos;
1828 typedef typename TFragmentStore::TContigPos TContigPos;
1868 TContigPos left = (*it).beginPos;
1869 TContigPos right = (*it).endPos;
2166 typedef typename TFragmentStore::TContigPos TContigPos;
2351 typedef typename TFragmentStore::TContigPos TContigPos;
2381 TContigPos left = it->beginPos;
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/
H A Dstore_align_intervals.h124 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in extractAlignIntervals() typedef
135 TContigPos beginPos = align.beginPos; in extractAlignIntervals()
136 TContigPos endPos = align.endPos; in extractAlignIntervals()
139 TContigPos help = beginPos; in extractAlignIntervals()
156 …TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos; // seqPos from Read projected to pos… in extractAlignIntervals()
171 TContigPos seqPos1 = 0; in extractAlignIntervals()
172 TContigPos gapPos1 = 0; in extractAlignIntervals()
173 TContigPos seqPos2 = firstSeqPos; in extractAlignIntervals()
174 TContigPos gapPos2 = firstGapPos; in extractAlignIntervals()
240 TContigPos lastGapPosBeforeGap1; in extractAlignIntervals()
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H A Dstore_all.h1561 typedef typename TFragmentStore::TContigPos TContigPos;
1683 typedef typename TFragmentStore::TContigPos TContigPos;
1748 TContigPos left = align.beginPos;
1749 TContigPos right = align.endPos;
1828 typedef typename TFragmentStore::TContigPos TContigPos;
1868 TContigPos left = (*it).beginPos;
1869 TContigPos right = (*it).endPos;
2166 typedef typename TFragmentStore::TContigPos TContigPos;
2351 typedef typename TFragmentStore::TContigPos TContigPos;
2381 TContigPos left = it->beginPos;
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/
H A Dstore_align_intervals.h124 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in extractAlignIntervals() typedef
135 TContigPos beginPos = align.beginPos; in extractAlignIntervals()
136 TContigPos endPos = align.endPos; in extractAlignIntervals()
139 TContigPos help = beginPos; in extractAlignIntervals()
156 …TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos; // seqPos from Read projected to pos… in extractAlignIntervals()
171 TContigPos seqPos1 = 0; in extractAlignIntervals()
172 TContigPos gapPos1 = 0; in extractAlignIntervals()
173 TContigPos seqPos2 = firstSeqPos; in extractAlignIntervals()
174 TContigPos gapPos2 = firstGapPos; in extractAlignIntervals()
240 TContigPos lastGapPosBeforeGap1; in extractAlignIntervals()
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H A Dstore_all.h1563 typedef typename TFragmentStore::TContigPos TContigPos;
1685 typedef typename TFragmentStore::TContigPos TContigPos;
1750 TContigPos left = align.beginPos;
1751 TContigPos right = align.endPos;
1830 typedef typename TFragmentStore::TContigPos TContigPos;
1870 TContigPos left = (*it).beginPos;
1871 TContigPos right = (*it).endPos;
2168 typedef typename TFragmentStore::TContigPos TContigPos;
2353 typedef typename TFragmentStore::TContigPos TContigPos;
2383 TContigPos left = it->beginPos;
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/dports/biology/seqan1/seqan-1.3.1/seqan/store/
H A Dstore_align_intervals.h128 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in extractAlignIntervals() typedef
139 TContigPos beginPos = align.beginPos; in extractAlignIntervals()
140 TContigPos endPos = align.endPos; in extractAlignIntervals()
143 TContigPos help = beginPos; in extractAlignIntervals()
160 …TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos; // seqPos from Read projected to pos… in extractAlignIntervals()
175 TContigPos seqPos1 = 0; in extractAlignIntervals()
176 TContigPos gapPos1 = 0; in extractAlignIntervals()
177 TContigPos seqPos2 = firstSeqPos; in extractAlignIntervals()
178 TContigPos gapPos2 = firstGapPos; in extractAlignIntervals()
244 TContigPos lastGapPosBeforeGap1; in extractAlignIntervals()
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H A Dstore_all.h1439 typedef typename TFragmentStore::TContigPos TContigPos;
1549 typedef typename TFragmentStore::TContigPos TContigPos;
1613 TContigPos left = align.beginPos;
1614 TContigPos right = align.endPos;
1678 typedef typename TFragmentStore::TContigPos TContigPos;
1700 TContigPos left = (*it).beginPos;
1701 TContigPos right = (*it).endPos;
1703 TContigPos cEnd = _max(left, right);
1885 typedef typename TFragmentStore::TContigPos TContigPos;
1912 TContigPos left = (*it).beginPos;
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H A Dstore_io_gff.h210 typedef typename TFragmentStore::TContigPos TContigPos; in _readOneAnnotation() typedef
267 TContigPos tmp = ctx.annotation.beginPos; in _readOneAnnotation()
479 typedef typename TFragmentStore::TContigPos TContigPos; in _writeOneAnnotation() typedef
496 TContigPos beginPos = annotation.beginPos; in _writeOneAnnotation()
497 TContigPos endPos = annotation.endPos; in _writeOneAnnotation()
501 TContigPos tmp = beginPos; in _writeOneAnnotation()
583 typedef typename TFragmentStore::TContigPos TContigPos; in _writeOneAnnotation() typedef
600 TContigPos beginPos = annotation.beginPos; in _writeOneAnnotation()
601 TContigPos endPos = annotation.endPos; in _writeOneAnnotation()
605 TContigPos tmp = beginPos; in _writeOneAnnotation()
H A Dstore_io_bam.h76 typedef typename TFragmentStore::TContigPos TContigPos; in read() typedef
80 typedef MatchMateInfo_<TContigPos, TId> TMatchMateInfo; in read()
172 typedef typename TFragmentStore::TContigPos TContigPos; in _readOneAlignment() typedef
193 TContigPos beginPos = record->core.pos; in _readOneAlignment()
207 TContigPos endPos; in _readOneAlignment()
213 TContigPos temp = beginPos; in _readOneAlignment()
227 TContigPos mPos = record->core.mpos; in _readOneAlignment()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar.h494 typename TContigPos,
602 TContigPos beginPos = record.beginPos;
613 TContigPos endPos;
693 TContigPos tmp = beginPos;
1067 typename TContigPos,
1077 TContigPos currWindowBegin,
1078 TContigPos currWindowEnd,
1133 …TContigPos groupEndCoordLocal = _min(groupEndPos+(TContigPos)options.realignAddBorder,(TContigPos)…
1238 typedef typename TFragmentStore::TContigPos TContigPos;
1289 TContigPos refStart;
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H A Dcasbar.cpp111 template<typename TFragmentStore, typename TContigPos, typename TOptions>
142 TContigPos currentWindowEnd, in copyNextWindowMatchesAndReads()
175 …>= mItBegin && _min((*mIt).beginPos,(*mIt).endPos) + (TContigPos)options.maxHitLength + (TContigPo… in copyNextWindowMatchesAndReads()
233 typedef typename TFragmentStore::TContigPos TContigPos; in applyPileupCorrection() typedef
258 TContigPos currentEnd = _max((*matchIt).beginPos,(*matchIt).endPos); in applyPileupCorrection()
370 typedef typename Position<TContigSeq>::Type TContigPos; in clipReads() typedef
395 TContigPos beginBefore = beginPos; in clipReads()
605 typedef typename TFragmentStore::TContigPos TContigPos; in detectSNPsForContig() typedef
619 TContigPos currentWindowBegin = 0; in detectSNPsForContig()
784 typedef typename TFragmentStore::TContigPos TContigPos; in detectSNPs() typedef
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/dports/biology/seqan1/seqan-1.3.1/demos/
H A Dsam2svg.cpp15 typedef TFragStore::TContigPos TContigPos; in main() typedef
35 TContigPos left = 0; in main()
36 TContigPos right = MaxValue<TContigPos>::VALUE; in main()
130 TContigPos right_ = right; in main()
131 if (right_ == MaxValue<TContigPos>::VALUE) in main()
/dports/biology/seqan1/seqan-1.3.1/apps/snp_store/
H A Dsnp_store.h1051 typedef typename TFragmentStore::TContigPos TContigPos;
1100 …TContigPos groupEndCoordLocal = _min(groupEndPos+(TContigPos)options.realignAddBorder,(TContigPos)…
1570 typedef typename TFragmentStore::TContigPos TContigPos;
1585 TContigPos genomeLen = (TContigPos)length(fragmentStore.contigStore[0].seq);
1645 …printAlignment(std::cout, Raw(), layout, fragmentStore, 0, (TContigPos)0, (TContigPos)maxPos, 0, 1…
1693 …printAlignment(std::cout, Raw(), layout, fragmentStore, 0, (TContigPos)0, (TContigPos)maxPos, 0, 1…
1721 …printAlignment(std::cout, Raw(), layout, fragmentStore, 0, (TContigPos)0, (TContigPos)maxPos, 0, 1…
1793 TContigPos refStart = (TContigPos)fragmentStore.alignedReadStore[numReads].beginPos;
2224 typedef typename TFragmentStore::TContigPos TContigPos;
2285 for(TContigPos candidatePos = 0; candidatePos < (TContigPos)length(genome); ++candidatePos)
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H A Dsnp_store.cpp258 TContigPos currentWindowEnd, in copyNextWindowMatchesAndReads()
340 typedef typename TFragmentStore::TContigPos TContigPos; in applyPileupCorrection() typedef
504 TContigPos beginBefore = beginPos; in clipReads()
656 typename TContigPos,
670 TContigPos currentBegin, in readMatchesFromGFF_Batch()
671 TContigPos currentEnd, in readMatchesFromGFF_Batch()
698 TContigPos genomeLen = length(genome); in readMatchesFromGFF_Batch()
805 TContigPos endPos = _parseReadNumber(*file,c); in readMatchesFromGFF_Batch()
1182 typedef typename TFragmentStore::TContigPos TContigPos; in detectSNPs() typedef
1333 TContigPos currentWindowBegin = 0; in detectSNPs()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/
H A Dsnp_store.h616 typename TContigPos,
771 TContigPos endPos = 0;
1328 typename TContigPos,
2392 typedef typename TFragmentStore::TContigPos TContigPos;
2444 …TContigPos groupEndCoordLocal = _min(groupEndPos+(TContigPos)options.realignAddBorder,(TContigPos)…
3788 typedef typename TFragmentStore::TContigPos TContigPos;
4575 typedef typename TFragmentStore::TContigPos TContigPos;
4951 typedef typename TFragmentStore::TContigPos TContigPos;
5584 typedef typename TFragmentStore::TContigPos TContigPos;
5733 typedef typename TFragmentStore::TContigPos TContigPos;
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H A Dsnp_store.cpp105 template<typename TFragmentStore, typename TContigPos, typename TOptions>
140 TContigPos currentWindowEnd, in copyNextWindowMatchesAndReads()
168 …>= mItBegin && _min((*mIt).beginPos,(*mIt).endPos) + (TContigPos)options.maxHitLength + (TContigPo… in copyNextWindowMatchesAndReads()
230 typedef typename TFragmentStore::TContigPos TContigPos; in applyPileupCorrection() typedef
371 typedef typename Position<TContigSeq>::Type TContigPos; in clipReads() typedef
396 TContigPos beginBefore = beginPos; in clipReads()
603 typedef typename TFragmentStore::TContigPos TContigPos; in detectSNPs() typedef
613 typedef String<String<TContigPos > > TPositions; in detectSNPs()
809 TContigPos currentWindowBegin = 0; in detectSNPs()
824 while(currentWindowBegin < (TContigPos)length(genomes[i])) in detectSNPs()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/
H A Dmapper_verifier.h218 template <typename TSpec, typename Traits, typename TContigPos, typename TMatch>
220 TContigPos & contigBegin, in _getMateContigPos()
221 TContigPos & contigEnd, in _getMateContigPos()
245 template <typename TSpec, typename Traits, typename TContigPos, typename TMatch>
247 TContigPos & contigBegin, in _getMateContigPos()
248 TContigPos & contigEnd, in _getMateContigPos()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rep_sep/
H A Dassembly_parser.h81 typedef typename TFragmentStore::TContigPos TContigPos; in parseContig() typedef
135 …d_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) { in parseContig()
140 …d_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) { in parseContig()
152 …(alignIt != alignItEnd && _min(alignIt->beginPos, alignIt->endPos) == static_cast<TContigPos>(p)) { in parseContig()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/unassigned_or_unused/
H A Dsam2svg.cpp124 typedef TFragStore::TContigPos TContigPos; in main() typedef
188 … int64_t r = (options.endPos == -1) ? std::numeric_limits<TContigPos>::max() : options.endPos; in main()
195 if (r != std::numeric_limits<TContigPos>::max()) in main()
199 if (r == std::numeric_limits<TContigPos>::max()) in main()
/dports/biology/seqan1/seqan-1.3.1/apps/rep_sep/
H A Dassembly_parser.h81 typedef typename TFragmentStore::TContigPos TContigPos; in parseContig() typedef
135 …d_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) { in parseContig()
140 …d_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) { in parseContig()
152 …(alignIt != alignItEnd && _min(alignIt->beginPos, alignIt->endPos) == static_cast<TContigPos>(p)) { in parseContig()
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A DoutputFormat.h178 typedef typename TFragmentStore::TContigPos TContigPos; in getErrorDistribution() typedef
184 TContigPos left, right; in getErrorDistribution()
221 typedef typename TFragmentStore::TContigPos TContigPos; in getErrorDistribution() typedef
245 TContigPos left = (*it).beginPos; in getErrorDistribution()
246 TContigPos right = (*it).endPos; in getErrorDistribution()
548 typedef typename TFragmentStore::TContigPos TContigPos; in dumpMatches() typedef
770 TContigPos left = (*it).beginPos; in dumpMatches()
771 TContigPos right = (*it).endPos; in dumpMatches()
920 TContigPos left = (*it).beginPos; in dumpMatches()
921 TContigPos right = (*it).endPos; in dumpMatches()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A DoutputFormat.h176 typedef typename TFragmentStore::TContigPos TContigPos; in getErrorDistribution() typedef
182 TContigPos left, right; in getErrorDistribution()
220 typedef typename TFragmentStore::TContigPos TContigPos; in getErrorDistribution() typedef
245 TContigPos left = (*it).beginPos; in getErrorDistribution()
246 TContigPos right = (*it).endPos; in getErrorDistribution()
295 typedef typename TFragmentStore::TContigPos TContigPos; in writeMismatchFile() typedef
306 TContigPos left = (*it).beginPos; in writeMismatchFile()
307 TContigPos right = (*it).endPos; in writeMismatchFile()
485 typedef typename TFragmentStore::TContigPos TContigPos; in dumpMatches() typedef
779 TContigPos left = ar.beginPos; in dumpMatches()
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/dports/biology/seqan1/seqan-1.3.1/apps/insegt/
H A Dread_gff.h36 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in readAnnotationsFromGFF() typedef
47 static const TContigPos INVALID_POS = TAnnotationStoreElement::INVALID_POS; in readAnnotationsFromGFF()
199 TContigPos beginPos; in readAnnotationsFromGFF()
200 TContigPos endPos; in readAnnotationsFromGFF()
H A Dread_gtf.h36 typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos; in readAnnotationsFromGTF() typedef
47 static const TContigPos INVALID_POS = TAnnotationStoreElement::INVALID_POS; in readAnnotationsFromGTF()
201 TContigPos beginPos; in readAnnotationsFromGTF()
202 TContigPos endPos; in readAnnotationsFromGTF()

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