/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/adapter/ |
H A D | ReadCollectionItf.hpp | 69 …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 );
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/adapter/ |
H A D | ReadCollectionItf.hpp | 69 …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 );
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/adapter/ |
H A D | ReadCollectionItf.hpp | 69 …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 );
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
H A D | NGS_ReadCollection.h | 128 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…
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H A D | CSRA1_Read.c | 113 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()
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H A D | CSRA1_Read.h | 64 bool wants_partial, 76 bool wants_partial, 89 bool wants_partial,
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H A D | NGS_ReadCollection.c | 199 …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 …]
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H A D | SRA_Read.h | 103 bool wants_partial; member 138 bool wants_partial, 154 bool wants_partial, 167 bool wants_partial,
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H A D | SRA_Read.c | 118 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 …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/ |
H A D | ReadCollectionItf.cpp | 217 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()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
H A D | NGS_ReadCollection.h | 128 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…
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H A D | CSRA1_Read.c | 113 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()
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H A D | CSRA1_Read.h | 64 bool wants_partial, 76 bool wants_partial, 89 bool wants_partial,
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H A D | NGS_ReadCollection.c | 199 …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 …]
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H A D | SRA_Read.h | 103 bool wants_partial; member 138 bool wants_partial, 154 bool wants_partial, 167 bool wants_partial,
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H A D | SRA_Read.c | 118 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 …]
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/ |
H A D | ReadCollectionItf.cpp | 217 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()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/ |
H A D | ReadCollectionItf.cpp | 217 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/test/test_engine/ |
H A D | ReadCollectionItf.hpp | 112 …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
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/test/test_engine/ |
H A D | ReadCollectionItf.hpp | 112 …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
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/test/test_engine/ |
H A D | ReadCollectionItf.hpp | 112 …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
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/itf/ |
H A D | ReadCollectionItf.h | 74 …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 );
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/itf/ |
H A D | ReadCollectionItf.h | 74 …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 );
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/itf/ |
H A D | ReadCollectionItf.h | 74 …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 );
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/dispatch/ |
H A D | ReadCollectionItf.cpp | 357 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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