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Searched refs:wants_partial (Results 1 – 25 of 41) sorted by relevance

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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/adapter/
H A DReadCollectionItf.hpp69 …virtual ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
70 …virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const …
71 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un…
100 bool wants_full, bool wants_partial, bool wants_unaligned );
102 bool wants_full, bool wants_partial, bool wants_unaligned );
104 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/adapter/
H A DReadCollectionItf.hpp69 …virtual ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
70 …virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const …
71 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un…
100 bool wants_full, bool wants_partial, bool wants_unaligned );
102 bool wants_full, bool wants_partial, bool wants_unaligned );
104 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/adapter/
H A DReadCollectionItf.hpp69 …virtual ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
70 …virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const …
71 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un…
100 bool wants_full, bool wants_partial, bool wants_unaligned );
102 bool wants_full, bool wants_partial, bool wants_unaligned );
104 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/
H A DNGS_ReadCollection.h128 bool wants_full, bool wants_partial, bool wants_unaligned );
131 bool wants_full, bool wants_partial, bool wants_unaligned );
138 bool wants_partial,
173 … ( NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_partial, bool wants_un…
176 bool wants_full, bool wants_partial, bool wants_unaligned );
177 …elf, ctx_t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un…
H A DCSRA1_Read.c113 self -> wants_partial = true; in CSRA1_ReadInit()
142 bool wants_partial, in CSRA1_ReadIteratorInit() argument
157 self -> wants_partial = wants_partial; in CSRA1_ReadIteratorInit()
170 bool wants_partial, in CSRA1_ReadIteratorMake() argument
192 …it ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in CSRA1_ReadIteratorMake()
220 bool wants_partial, in CSRA1_ReadIteratorMakeRange() argument
242 …it ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in CSRA1_ReadIteratorMakeRange()
272 bool wants_partial, in CSRA1_ReadIteratorMakeReadGroup() argument
283 wants_partial, in CSRA1_ReadIteratorMakeReadGroup()
526 if ( ( cat == NGS_ReadCategory_partiallyAligned && ! self -> wants_partial ) in CSRA1_ReadIteratorNext()
H A DCSRA1_Read.h64 bool wants_partial,
76 bool wants_partial,
89 bool wants_partial,
H A DNGS_ReadCollection.c199 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un… in NGS_ReadCollection_v1_get_reads() argument
202 … * ret = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_get_reads()
211 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un… in NGS_ReadCollection_v1_get_read_count() argument
214 …et = NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_get_read_count()
226 …ollectionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_read_range()
466 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReads() argument
475 return VT ( self, get_reads ) ( self, ctx, wants_full, wants_partial, wants_unaligned ); in NGS_ReadCollectionGetReads()
499 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReadCount() argument
508 … return VT ( self, get_read_count ) ( self, ctx, wants_full, wants_partial, wants_unaligned ); in NGS_ReadCollectionGetReadCount()
515 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReadRange() argument
[all …]
H A DSRA_Read.h103 bool wants_partial; member
138 bool wants_partial,
154 bool wants_partial,
167 bool wants_partial,
H A DSRA_Read.c118 self -> wants_partial = true; in SRA_ReadInit()
132 bool wants_partial, in SRA_ReadIteratorInit() argument
146 self -> wants_partial = wants_partial; in SRA_ReadIteratorInit()
557 bool wants_partial, in SRA_ReadIteratorMake() argument
578 …rInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in SRA_ReadIteratorMake()
604 bool wants_partial, in SRA_ReadIteratorMakeRange() argument
625 …rInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in SRA_ReadIteratorMakeRange()
653 bool wants_partial, in SRA_ReadIteratorMakeReadGroup() argument
664 wants_partial, in SRA_ReadIteratorMakeReadGroup()
711 ! self -> wants_partial || in SRA_ReadIteratorNext()
[all …]
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/
H A DReadCollectionItf.cpp217 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_reads() argument
222 ReadItf * val = self -> getReads ( wants_full, wants_partial, wants_unaligned ); in get_reads()
234 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_count() argument
239 return self -> getReadCount ( wants_full, wants_partial, wants_unaligned ); in get_read_count()
250 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_range() argument
255 … ReadItf * val = self -> getReadRange ( first, count, wants_full, wants_partial, wants_unaligned ); in get_read_range()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/
H A DNGS_ReadCollection.h128 bool wants_full, bool wants_partial, bool wants_unaligned );
131 bool wants_full, bool wants_partial, bool wants_unaligned );
138 bool wants_partial,
173 … ( NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_partial, bool wants_un…
176 bool wants_full, bool wants_partial, bool wants_unaligned );
177 …elf, ctx_t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un…
H A DCSRA1_Read.c113 self -> wants_partial = true; in CSRA1_ReadInit()
142 bool wants_partial, in CSRA1_ReadIteratorInit() argument
157 self -> wants_partial = wants_partial; in CSRA1_ReadIteratorInit()
170 bool wants_partial, in CSRA1_ReadIteratorMake() argument
192 …it ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in CSRA1_ReadIteratorMake()
220 bool wants_partial, in CSRA1_ReadIteratorMakeRange() argument
242 …it ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in CSRA1_ReadIteratorMakeRange()
272 bool wants_partial, in CSRA1_ReadIteratorMakeReadGroup() argument
283 wants_partial, in CSRA1_ReadIteratorMakeReadGroup()
526 if ( ( cat == NGS_ReadCategory_partiallyAligned && ! self -> wants_partial ) in CSRA1_ReadIteratorNext()
H A DCSRA1_Read.h64 bool wants_partial,
76 bool wants_partial,
89 bool wants_partial,
H A DNGS_ReadCollection.c199 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un… in NGS_ReadCollection_v1_get_reads() argument
202 … * ret = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_get_reads()
211 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un… in NGS_ReadCollection_v1_get_read_count() argument
214 …et = NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_get_read_count()
226 …ollectionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, wants_unalign… in NGS_ReadCollection_v1_read_range()
466 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReads() argument
475 return VT ( self, get_reads ) ( self, ctx, wants_full, wants_partial, wants_unaligned ); in NGS_ReadCollectionGetReads()
499 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReadCount() argument
508 … return VT ( self, get_read_count ) ( self, ctx, wants_full, wants_partial, wants_unaligned ); in NGS_ReadCollectionGetReadCount()
515 bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollectionGetReadRange() argument
[all …]
H A DSRA_Read.h103 bool wants_partial; member
138 bool wants_partial,
154 bool wants_partial,
167 bool wants_partial,
H A DSRA_Read.c118 self -> wants_partial = true; in SRA_ReadInit()
132 bool wants_partial, in SRA_ReadIteratorInit() argument
146 self -> wants_partial = wants_partial; in SRA_ReadIteratorInit()
557 bool wants_partial, in SRA_ReadIteratorMake() argument
578 …rInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in SRA_ReadIteratorMake()
604 bool wants_partial, in SRA_ReadIteratorMakeRange() argument
625 …rInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unalign… in SRA_ReadIteratorMakeRange()
653 bool wants_partial, in SRA_ReadIteratorMakeReadGroup() argument
664 wants_partial, in SRA_ReadIteratorMakeReadGroup()
711 ! self -> wants_partial || in SRA_ReadIteratorNext()
[all …]
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/
H A DReadCollectionItf.cpp217 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_reads() argument
222 ReadItf * val = self -> getReads ( wants_full, wants_partial, wants_unaligned ); in get_reads()
234 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_count() argument
239 return self -> getReadCount ( wants_full, wants_partial, wants_unaligned ); in get_read_count()
250 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_range() argument
255 … ReadItf * val = self -> getReadRange ( first, count, wants_full, wants_partial, wants_unaligned ); in get_read_range()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/
H A DReadCollectionItf.cpp217 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_reads() argument
222 ReadItf * val = self -> getReads ( wants_full, wants_partial, wants_unaligned ); in get_reads()
234 bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_count() argument
239 return self -> getReadCount ( wants_full, wants_partial, wants_unaligned ); in get_read_count()
250 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) in get_read_range() argument
255 … ReadItf * val = self -> getReadRange ( first, count, wants_full, wants_partial, wants_unaligned ); in get_read_range()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/test/test_engine/
H A DReadCollectionItf.hpp112 …virtual ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned … in getReads() argument
117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() argument
122 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un… in getReadRange() argument
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/test/test_engine/
H A DReadCollectionItf.hpp112 …virtual ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned … in getReads() argument
117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() argument
122 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un… in getReadRange() argument
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/test/test_engine/
H A DReadCollectionItf.hpp112 …virtual ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned … in getReads() argument
117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() argument
122 … getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_un… in getReadRange() argument
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
75 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
77 uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
75 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
77 uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
75 …eadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_un…
77 uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/dispatch/
H A DReadCollectionItf.cpp357 bool wants_partial = ( categories & Read :: partiallyAligned ) != 0; in getReads() local
359 …NGS_Read_v1 * ret = ( * vt -> get_reads ) ( self, & err, wants_full, wants_partial, wants_unalign… in getReads()
380 bool wants_partial = ( categories & Read :: partiallyAligned ) != 0; in getReadCount() local
382 …uint64_t ret = ( * vt -> get_read_count ) ( self, & err, wants_full, wants_partial, wants_unalign… in getReadCount()
423 bool wants_partial = ( categories & Read :: partiallyAligned ) != 0; in getReadRange() local
425 …= ( * vt -> get_read_range ) ( self, & err, first, count, wants_full, wants_partial, wants_unalign… in getReadRange()

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