| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bam_io/ |
| H A D | test_write_sam.h | 51 StringSet<CharString> contigNameStore; in SEQAN_DEFINE_TEST() local
52 appendValue(contigNameStore, "REF"); in SEQAN_DEFINE_TEST()
53 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in SEQAN_DEFINE_TEST()
54 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in SEQAN_DEFINE_TEST()
88 StringSet<CharString> contigNameStore; in SEQAN_DEFINE_TEST() local
89 appendValue(contigNameStore, "REF"); in SEQAN_DEFINE_TEST()
90 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in SEQAN_DEFINE_TEST()
91 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in SEQAN_DEFINE_TEST()
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| H A D | test_write_bam.h | 53 StringSet<CharString> contigNameStore; in SEQAN_DEFINE_TEST() local
54 appendValue(contigNameStore, "REFERENCE"); in SEQAN_DEFINE_TEST()
55 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in SEQAN_DEFINE_TEST()
56 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in SEQAN_DEFINE_TEST()
98 StringSet<CharString> contigNameStore; in SEQAN_DEFINE_TEST() local
99 appendValue(contigNameStore, "REFERENCE"); in SEQAN_DEFINE_TEST()
100 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in SEQAN_DEFINE_TEST()
101 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in SEQAN_DEFINE_TEST()
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| H A D | test_bam_io_context.h | 66 …BamIOContext<TNameStore, TNameStoreCache> bamIOContext(store.contigNameStore, store.contigNameStor… in SEQAN_DEFINE_TEST()
67 SEQAN_ASSERT_EQ(&store.contigNameStore, &contigNames(bamIOContext)); in SEQAN_DEFINE_TEST()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/realign/ |
| H A D | test_realign.cpp | 66 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
112 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
161 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
213 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
281 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
355 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
414 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
474 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
530 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
585 appendValue(store.contigNameStore, "ref"); in SEQAN_DEFINE_TEST()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seq_io/ |
| H A D | bam_sam.h | 383 StringSet<CharString> contigNameStore; in _writeRecord() local
384 appendValue(contigNameStore, "*"); in _writeRecord()
385 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in _writeRecord()
386 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in _writeRecord()
418 StringSet<CharString> contigNameStore; in _writeRecord() local
419 appendValue(contigNameStore, "*"); in _writeRecord()
420 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in _writeRecord()
421 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in _writeRecord()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/seq_io/ |
| H A D | bam_sam.h | 383 StringSet<CharString> contigNameStore; in _writeRecord() local
384 appendValue(contigNameStore, "*"); in _writeRecord()
385 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in _writeRecord()
386 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in _writeRecord()
418 StringSet<CharString> contigNameStore; in _writeRecord() local
419 appendValue(contigNameStore, "*"); in _writeRecord()
420 NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore); in _writeRecord()
421 BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache); in _writeRecord()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rabema/ |
| H A D | rabema_build_gold_standard.cpp | 218 StringSet<CharString> const & contigNameStore, in intervalizeAndDumpErrorCurves() argument
342 gsiDistance, contigNameStore[it2->contigId], in intervalizeAndDumpErrorCurves()
754 StringSet<CharString> const & contigNameStore, in matchesToErrorFunction() argument
851 std::cerr << contigNameStore[record.rID] << " (" << record.rID + 1 << "/" in matchesToErrorFunction()
852 << length(contigNameStore) << ") "; in matchesToErrorFunction()
858 if (!getIdByName(faiRefId, faiIndex, contigNameStore[record.rID])) in matchesToErrorFunction()
860 … std::cerr << "Reference sequence " << contigNameStore[record.rID] << " not known in FAI file.\n"; in matchesToErrorFunction()
869 std::cerr << "Could not load sequence " << contigNameStore[record.rID] in matchesToErrorFunction()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
| H A D | store_io_bam.h | 379 bamHeader.target_name[i] = new char[length(fragStore.contigNameStore[i]) + 1]; in write()
380 …cpy(bamHeader.target_name[i], toCString(fragStore.contigNameStore[i]), length(fragStore.contigName… in write()
510 bamRecord.core.tid = (*it).contigId < length(store.contigNameStore) ? (*it).contigId : -1; in _writeAlignments()
544 … bamRecord.core.mtid = ((*mit).contigId < length(store.contigNameStore)) ? (*mit).contigId : -1; in _writeAlignments()
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| H A D | store_io_sam.h | 886 TContigNameIter nit = begin(store.contigNameStore, Standard()); in _writeHeader()
887 TContigNameIter nitEnd = end(store.contigNameStore, Standard()); in _writeHeader()
1024 if ((*it).contigId < length(store.contigNameStore)) in _writeAlignments()
1025 _streamWrite(target, store.contigNameStore[(*it).contigId]); in _writeAlignments()
1077 if ((*mit).contigId < length(store.contigNameStore)) in _writeAlignments()
1078 _streamWrite(target, store.contigNameStore[(*mit).contigId]); in _writeAlignments()
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| H A D | store_io_gff.h | 484 if (annotation.contigId < length(store.contigNameStore)) in _writeOneAnnotation()
485 _streamWrite(target, store.contigNameStore[annotation.contigId]); in _writeOneAnnotation()
588 if (annotation.contigId < length(store.contigNameStore)) in _writeOneAnnotation()
589 _streamWrite(target, store.contigNameStore[annotation.contigId]); in _writeOneAnnotation()
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| H A D | store_io.h | 476 appendValue(fragStore.contigNameStore, eid, Generous() ); in read()
693 noNamesPresent = (length(fragStore.contigNameStore) == 0); in write()
701 _streamWrite(target, value(fragStore.contigNameStore, idCount)); in write()
824 for (unsigned i = 0; i < length(store.contigNameStore); ++i) in writeContigs()
825 write(file, store.contigStore[i].seq, store.contigNameStore[i], TFormat()); in writeContigs()
875 resize(store.contigNameStore, seqOfs + seqCount, Generous()); in loadContigs()
886 assignCroppedSeqId(store.contigNameStore[seqOfs + i], multiSeqFile[i], contigFile.format); in loadContigs()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/insegt/ |
| H A D | create_gff.h | 72 readOutput << getValue(fragStore.contigNameStore, getValue(itCountStore).contigId) in createReadCountGFF()
218 annoOutput << getValue(fragStore.contigNameStore, getValue(itAnno).contigId) << '\t'; in createAnnoCountGFF()
319 tupleOutput << getValue(fragStore.contigNameStore, currentElement.contigId) << '\t'; in createTupleCountGFF()
354 tupleOutput << getValue(fragStore.contigNameStore, currentElement.contigId) << '\t'; in createTupleCountGFF()
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| /dports/biology/seqan1/seqan-1.3.1/apps/insegt/ |
| H A D | read_gff.h | 211 itContigName = begin(me.contigNameStore); in readAnnotationsFromGFF()
212 itContigNameEnd = end(me.contigNameStore); in readAnnotationsFromGFF()
219 contigId = position(itContigName, me.contigNameStore); in readAnnotationsFromGFF()
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| H A D | read_gtf.h | 212 itContigName = begin(me.contigNameStore); in readAnnotationsFromGTF()
213 itContigNameEnd = end(me.contigNameStore); in readAnnotationsFromGTF()
220 contigId = position(itContigName, me.contigNameStore); in readAnnotationsFromGTF()
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| H A D | create_gff.h | 72 _streamWrite(readOutput, getValue(me.contigNameStore, getValue(itCountStore).contigId) ); in createReadCountGFF()
233 _streamWrite(annoOutput, getValue(me.contigNameStore, getValue(itAnno).contigId)); in createAnnoCountGFF()
348 _streamWrite(tupleOutput, getValue(me.contigNameStore, currentElement.contigId)); in createTupleCountGFF()
399 _streamWrite(tupleOutput, getValue(me.contigNameStore, currentElement.contigId)); in createTupleCountGFF()
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| /dports/biology/seqan1/seqan-1.3.1/demos/ |
| H A D | sequence_length.cpp | 27 …std::cout << fragmentStore.contigNameStore[i] << "\t" << length(fragmentStore.contigStore[i].seq) … in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/consensus_alignment/ |
| H A D | with_positions.cpp | 16 appendValue(store.contigNameStore, "ref"); in main()
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/consensus/ |
| H A D | consensus_alignment.cpp | 35 resize(store.contigNameStore, 1); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/consensus/ |
| H A D | consensus_alignment.cpp | 35 resize(store.contigNameStore, 1); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
| H A D | store_io.h | 525 appendValue(fragStore.contigNameStore, eid, Generous()); in read()
779 if (!empty(fragStore.contigNameStore) && !empty(fragStore.contigNameStore[idCount])) in write()
782 write(iter, fragStore.contigNameStore[idCount]); in write()
933 for (unsigned i = 0; i < length(store.contigNameStore); ++i) in writeContigs()
934 writeRecord(file, store.contigNameStore[i], store.contigStore[i].seq); in writeContigs()
1021 appendValue(store.contigNameStore, meta, Generous()); in loadContigs()
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| H A D | store_io_ucsc.h | 215 if (annotation.contigId < length(fragStore.contigNameStore)) in _fillAnnotationRecord()
216 record.contigName = fragStore.contigNameStore[annotation.contigId]; in _fillAnnotationRecord()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/ |
| H A D | store_io.h | 525 appendValue(fragStore.contigNameStore, eid, Generous()); in read()
779 if (!empty(fragStore.contigNameStore) && !empty(fragStore.contigNameStore[idCount])) in write()
782 write(iter, fragStore.contigNameStore[idCount]); in write()
933 for (unsigned i = 0; i < length(store.contigNameStore); ++i) in writeContigs()
934 writeRecord(file, store.contigNameStore[i], store.contigStore[i].seq); in writeContigs()
1021 appendValue(store.contigNameStore, meta, Generous()); in loadContigs()
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| H A D | store_io_ucsc.h | 215 if (annotation.contigId < length(fragStore.contigNameStore)) in _fillAnnotationRecord()
216 record.contigName = fragStore.contigNameStore[annotation.contigId]; in _fillAnnotationRecord()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/ |
| H A D | store_io.h | 525 appendValue(fragStore.contigNameStore, eid, Generous()); in read()
779 if (!empty(fragStore.contigNameStore) && !empty(fragStore.contigNameStore[idCount])) in write()
782 write(iter, fragStore.contigNameStore[idCount]); in write()
912 for (unsigned i = 0; i < length(store.contigNameStore); ++i) in writeContigs()
913 writeRecord(file, store.contigNameStore[i], store.contigStore[i].seq); in writeContigs()
978 appendValue(store.contigNameStore, meta, Generous()); in loadContigs()
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| H A D | store_io_ucsc.h | 215 if (annotation.contigId < length(fragStore.contigNameStore)) in _fillAnnotationRecord()
216 record.contigName = fragStore.contigNameStore[annotation.contigId]; in _fillAnnotationRecord()
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