Searched refs:graph_range (Results 1 – 4 of 4) sorted by relevance
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/bam/ |
| H A D | bamloader_impl.cpp | 2124 auto graph_range = GetChunkGraphRange(range_id); in LoadPileupChunk() local
2129 SPileupGraphCreator gg(GetRefSeq_id(), graph_range); in LoadPileupChunk()
2136 size_t count = m_File->GetBamDb().CollectPileup(ss, GetRefSeqId(), graph_range, in LoadPileupChunk()
2345 auto graph_range = GetChunkGraphRange(range_id); in LoadPileupChunk() local
2351 SBaseStats ss(graph_range.GetLength()); in LoadPileupChunk()
2356 CBamAlignIterator ait(*m_File, GetRefSeqId(), graph_range.GetFrom(), graph_range.GetLength()); in LoadPileupChunk()
2370 TSeqPos ss_pos = align_pos - graph_range.GetFrom(); in LoadPileupChunk()
2430 TSignedSeqPos ss_pos = align_pos - graph_range.GetFrom(); in LoadPileupChunk()
2543 loc.SetFrom(graph_range.GetFrom()); in LoadPileupChunk()
2544 loc.SetTo(graph_range.GetTo()); in LoadPileupChunk()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/ |
| H A D | test_csra_loader.cpp | 1299 CRange<TSeqPos> graph_range = graph.GetLoc().GetTotalRange(); in BOOST_AUTO_TEST_CASE() local
1301 graph_range.IntersectionWith(CRange<TSeqPos>(from, to)); in BOOST_AUTO_TEST_CASE()
1304 TSeqPos i = pos - graph_range.GetFrom(); in BOOST_AUTO_TEST_CASE()
1505 CRange<TSeqPos> graph_range = graph.GetLoc().GetTotalRange(); in BOOST_AUTO_TEST_CASE() local
1507 graph_range.IntersectionWith(CRange<TSeqPos>(from, to)); in BOOST_AUTO_TEST_CASE()
1510 TSeqPos i = pos - graph_range.GetFrom(); in BOOST_AUTO_TEST_CASE()
1690 CRange<TSeqPos> graph_range = graph.GetLoc().GetTotalRange(); in BOOST_AUTO_TEST_CASE() local
1692 graph_range.IntersectionWith(CRange<TSeqPos>(from, to)); in BOOST_AUTO_TEST_CASE()
1695 TSeqPos i = pos - graph_range.GetFrom(); in BOOST_AUTO_TEST_CASE()
1880 graph_range.IntersectionWith(CRange<TSeqPos>(from, to)); in BOOST_AUTO_TEST_CASE()
[all …]
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/ |
| H A D | bamread.cpp | 1349 CRange<TSeqPos> graph_range, in CollectPileup() argument
1355 values.initialize(graph_range, intron_mode); in CollectPileup()
1359 CBamAlignIterator ait(*this, ref_id, graph_range.GetFrom(), graph_range.GetLength()); in CollectPileup()
1373 if ( ref_pos >= graph_range.GetToOpen() ) { in CollectPileup()
1437 _ASSERT((values.m_RefFrom-graph_range.GetFrom())%16 == 0); in CollectPileup()
1446 if ( ref_pos >= graph_range.GetToOpen() ) { in CollectPileup()
1511 _ASSERT((values.m_RefFrom-graph_range.GetFrom())%16 == 0); in CollectPileup()
1518 if ( callback && graph_range.GetToOpen() != values.m_RefFrom ) { in CollectPileup()
1519 TSeqPos flush = graph_range.GetToOpen() - values.m_RefFrom; in CollectPileup()
1528 _ASSERT(values.m_RefFrom == graph_range.GetToOpen()); in CollectPileup()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/bam/ |
| H A D | bamread.hpp | 488 CRange<TSeqPos> graph_range,
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