/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
H A D | NGS_Reference.c | 190 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_alignments() local 226 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_align_slice() local 303 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_pileups() local 321 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_pileup_slice() local 584 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignments() 601 …enceGetAlignmentCount ( NGS_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in NGS_ReferenceGetAlignmentCount() 623 bool wants_secondary ) in NGS_ReferenceGetAlignmentSlice() 700 bool wants_secondary ) in NGS_ReferenceGetPileupSlice() 722 bool wants_secondary, in NGS_ReferenceGetFilteredPileupSlice() 870 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in Null_ReferenceGetAlignments() [all …]
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H A D | NGS_ReadCollection.c | 151 …nst NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_alignments() 163 …nst NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_align_count() 175 …, NGS_ErrBlock_v1 * err, uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_align_range() 400 bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignments() 432 …etAlignmentCount ( NGS_ReadCollection * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignmentCount() 448 bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignmentRange()
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H A D | SRA_ReadCollection.c | 190 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignments() 210 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignmentCount() 219 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignmentRange()
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H A D | SRA_DB_ReadCollection.c | 202 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignments() 222 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignmentCount() 229 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignmentRange()
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H A D | CSRA1_Reference.c | 462 …ignments ( CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetAlignments() 510 …lignmentCount ( const CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in CSRA1_ReferenceGetAlignmentCount() 643 bool wants_secondary, in CSRA1_ReferenceGetAlignmentSlice() 729 …tPileups ( CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetPileups() 757 …f, ctx_t ctx, uint64_t offset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetPileupSlice()
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H A D | CSRA1_ReadCollection.c | 363 bool wants_primary, bool wants_secondary ) in CSRA1_ReadCollectionGetAlignments() 412 bool wants_primary, bool wants_secondary ) in CSRA1_ReadCollectionGetAlignmentCount() 441 bool wants_secondary ) in CSRA1_ReadCollectionGetAlignmentRange()
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H A D | BAM_ReadCollection.c | 253 …erenceGetAlignments(NGS_Reference *const base, ctx_t ctx, bool wants_primary, bool wants_secondary) in BAM_ReferenceGetAlignments() 266 …lignmentCount(NGS_Reference const *const base, ctx_t ctx, bool wants_primary, bool wants_secondary) in BAM_ReferenceGetAlignmentCount() 295 bool wants_secondary, in BAM_ReferenceGetAlignmentSlice() 352 …ReferenceGetPileups(NGS_Reference *const base, ctx_t ctx, bool wants_primary, bool wants_secondary) in BAM_ReferenceGetPileups() 467 …ts(NGS_ReadCollection *const vp, ctx_t ctx, bool const wants_primary, bool const wants_secondary) { in BAM_ReadCollectionAlignments() 488 …nt(NGS_ReadCollection *const vp, ctx_t ctx, bool const wants_primary, bool const wants_secondary) { in BAM_ReadCollectionAlignmentCount() 495 …uint64_t const first, uint64_t const count, bool const wants_primary, bool const wants_secondary) { in BAM_ReadCollectionAlignmentRange()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
H A D | NGS_Reference.c | 190 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_alignments() local 226 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_align_slice() local 303 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_pileups() local 321 bool wants_secondary = ( flags & NGS_ReferenceAlignFlags_wants_secondary ) != 0; in ITF_Reference_v1_get_filtered_pileup_slice() local 584 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignments() 601 …enceGetAlignmentCount ( NGS_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in NGS_ReferenceGetAlignmentCount() 623 bool wants_secondary ) in NGS_ReferenceGetAlignmentSlice() 700 bool wants_secondary ) in NGS_ReferenceGetPileupSlice() 722 bool wants_secondary, in NGS_ReferenceGetFilteredPileupSlice() 870 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in Null_ReferenceGetAlignments() [all …]
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H A D | NGS_ReadCollection.c | 151 …nst NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_alignments() 163 …nst NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_align_count() 175 …, NGS_ErrBlock_v1 * err, uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) in NGS_ReadCollection_v1_get_align_range() 400 bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignments() 432 …etAlignmentCount ( NGS_ReadCollection * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignmentCount() 448 bool wants_primary, bool wants_secondary ) in NGS_ReadCollectionGetAlignmentRange()
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H A D | SRA_ReadCollection.c | 190 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignments() 210 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignmentCount() 219 bool wants_primary, bool wants_secondary ) in SRA_ReadCollectionGetAlignmentRange()
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H A D | SRA_DB_ReadCollection.c | 202 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignments() 222 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignmentCount() 229 bool wants_primary, bool wants_secondary ) in SRA_DB_ReadCollectionGetAlignmentRange()
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H A D | CSRA1_Reference.c | 462 …ignments ( CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetAlignments() 510 …lignmentCount ( const CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary ) in CSRA1_ReferenceGetAlignmentCount() 643 bool wants_secondary, in CSRA1_ReferenceGetAlignmentSlice() 729 …tPileups ( CSRA1_Reference * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetPileups() 757 …f, ctx_t ctx, uint64_t offset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t f… in CSRA1_ReferenceGetPileupSlice()
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H A D | CSRA1_ReadCollection.c | 363 bool wants_primary, bool wants_secondary ) in CSRA1_ReadCollectionGetAlignments() 412 bool wants_primary, bool wants_secondary ) in CSRA1_ReadCollectionGetAlignmentCount() 441 bool wants_secondary ) in CSRA1_ReadCollectionGetAlignmentRange()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 160 bool wants_primary, bool wants_secondary ) in get_alignment_count() 193 bool wants_primary, bool wants_secondary ) in get_alignments() 210 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_align_slice() 244 bool wants_primary, bool wants_secondary ) in get_pileups() 278 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_pileup_slice()
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H A D | ReadCollectionItf.cpp | 150 bool wants_primary, bool wants_secondary ) in get_alignments() 167 bool wants_primary, bool wants_secondary ) in get_align_count() 183 uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) in get_align_range()
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 160 bool wants_primary, bool wants_secondary ) in get_alignment_count() 193 bool wants_primary, bool wants_secondary ) in get_alignments() 210 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_align_slice() 244 bool wants_primary, bool wants_secondary ) in get_pileups() 278 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_pileup_slice()
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H A D | ReadCollectionItf.cpp | 150 bool wants_primary, bool wants_secondary ) in get_alignments() 167 bool wants_primary, bool wants_secondary ) in get_align_count() 183 uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) in get_align_range()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 160 bool wants_primary, bool wants_secondary ) in get_alignment_count() 193 bool wants_primary, bool wants_secondary ) in get_alignments() 210 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_align_slice() 244 bool wants_primary, bool wants_secondary ) in get_pileups() 278 … int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) in get_pileup_slice()
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H A D | ReadCollectionItf.cpp | 150 bool wants_primary, bool wants_secondary ) in get_alignments() 167 bool wants_primary, bool wants_secondary ) in get_align_count() 183 uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) in get_align_range()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/dispatch/ |
H A D | ReferenceItf.cpp | 273 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentCount() local 320 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignments() local 354 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentSlice() local 416 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileups() local 484 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileupSlice() local
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H A D | ReadCollectionItf.cpp | 268 bool wants_secondary in getAlignments() local 291 bool wants_secondary in getAlignmentCount() local 314 bool wants_secondary in getAlignmentRange() local
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/dispatch/ |
H A D | ReferenceItf.cpp | 273 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentCount() local 320 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignments() local 354 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentSlice() local 416 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileups() local 484 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileupSlice() local
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H A D | ReadCollectionItf.cpp | 268 bool wants_secondary in getAlignments() local 291 bool wants_secondary in getAlignmentCount() local 314 bool wants_secondary in getAlignmentRange() local
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/dispatch/ |
H A D | ReferenceItf.cpp | 273 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentCount() local 320 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignments() local 354 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getAlignmentSlice() local 416 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileups() local 484 bool wants_secondary = ( categories & Alignment :: secondaryAlignment ) != 0; in getPileupSlice() local
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H A D | ReadCollectionItf.cpp | 268 bool wants_secondary in getAlignments() local 291 bool wants_secondary in getAlignmentCount() local 314 bool wants_secondary in getAlignmentRange() local
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