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Searched defs:wants_secondary (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/
H A DNGS_Reference.c190 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 …]
H A DNGS_ReadCollection.c151 …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()
H A DSRA_ReadCollection.c190 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()
H A DSRA_DB_ReadCollection.c202 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()
H A DCSRA1_Reference.c462 …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()
H A DCSRA1_ReadCollection.c363 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()
H A DBAM_ReadCollection.c253 …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()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/
H A DNGS_Reference.c190 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 …]
H A DNGS_ReadCollection.c151 …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()
H A DSRA_ReadCollection.c190 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()
H A DSRA_DB_ReadCollection.c202 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()
H A DCSRA1_Reference.c462 …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()
H A DCSRA1_ReadCollection.c363 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()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/
H A DReferenceItf.cpp160 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()
H A DReadCollectionItf.cpp150 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()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/
H A DReferenceItf.cpp160 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()
H A DReadCollectionItf.cpp150 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()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/
H A DReferenceItf.cpp160 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()
H A DReadCollectionItf.cpp150 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()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/dispatch/
H A DReferenceItf.cpp273 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
H A DReadCollectionItf.cpp268 bool wants_secondary in getAlignments() local
291 bool wants_secondary in getAlignmentCount() local
314 bool wants_secondary in getAlignmentRange() local
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/dispatch/
H A DReferenceItf.cpp273 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
H A DReadCollectionItf.cpp268 bool wants_secondary in getAlignments() local
291 bool wants_secondary in getAlignmentCount() local
314 bool wants_secondary in getAlignmentRange() local
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/dispatch/
H A DReferenceItf.cpp273 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
H A DReadCollectionItf.cpp268 bool wants_secondary in getAlignments() local
291 bool wants_secondary in getAlignmentCount() local
314 bool wants_secondary in getAlignmentRange() local

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