/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 …virtual ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_parti… 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 …virtual ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_parti… 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 …virtual ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_parti… 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 ); 137 bool wants_full, 173 …* get_reads ) ( NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_part… 176 bool wants_full, bool wants_partial, bool wants_unaligned ); 177 …READCOLLECTION * self, ctx_t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_part…
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H A D | CSRA1_Read.c | 112 self -> wants_full = true; in CSRA1_ReadInit() 141 bool wants_full, in CSRA1_ReadIteratorInit() argument 156 self -> wants_full = wants_full; in CSRA1_ReadIteratorInit() 169 bool wants_full, in CSRA1_ReadIteratorMake() argument 192 …eadIteratorInit ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, … in CSRA1_ReadIteratorMake() 219 bool wants_full, in CSRA1_ReadIteratorMakeRange() argument 242 …eadIteratorInit ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, … in CSRA1_ReadIteratorMakeRange() 271 bool wants_full, in CSRA1_ReadIteratorMakeReadGroup() argument 282 wants_full, in CSRA1_ReadIteratorMakeReadGroup() 477 if ( self -> wants_full ) in CSRA1_ReadIteratorNext()
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H A D | CSRA1_Read.h | 63 bool wants_full, 75 bool wants_full, 88 bool wants_full,
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H A D | NGS_ReadCollection.c | 199 …eads ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… in NGS_ReadCollection_v1_get_reads() argument 202 …ON_FAIL ( struct NGS_Read * ret = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wan… in NGS_ReadCollection_v1_get_reads() 211 …ount ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… in NGS_ReadCollection_v1_get_read_count() argument 214 …ON_FAIL ( uint64_t ret = NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_pa… in NGS_ReadCollection_v1_get_read_count() 226 …t = NGS_ReadCollectionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, … 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 | 102 bool wants_full; member 137 bool wants_full, 153 bool wants_full, 166 bool wants_full,
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H A D | SRA_Read.c | 117 self -> wants_full = true; in SRA_ReadInit() 131 bool wants_full, in SRA_ReadIteratorInit() argument 145 self -> wants_full = wants_full; in SRA_ReadIteratorInit() 556 bool wants_full, in SRA_ReadIteratorMake() argument 578 …TRY ( SRA_ReadIteratorInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_p… in SRA_ReadIteratorMake() 603 bool wants_full, in SRA_ReadIteratorMakeRange() argument 625 …TRY ( SRA_ReadIteratorInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_p… in SRA_ReadIteratorMakeRange() 652 bool wants_full, in SRA_ReadIteratorMakeReadGroup() argument 663 wants_full, in SRA_ReadIteratorMakeReadGroup() 710 if ( ! self -> wants_full || 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 ); 137 bool wants_full, 173 …* get_reads ) ( NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_part… 176 bool wants_full, bool wants_partial, bool wants_unaligned ); 177 …READCOLLECTION * self, ctx_t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_part…
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H A D | CSRA1_Read.c | 112 self -> wants_full = true; in CSRA1_ReadInit() 141 bool wants_full, in CSRA1_ReadIteratorInit() argument 156 self -> wants_full = wants_full; in CSRA1_ReadIteratorInit() 169 bool wants_full, in CSRA1_ReadIteratorMake() argument 192 …eadIteratorInit ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, … in CSRA1_ReadIteratorMake() 219 bool wants_full, in CSRA1_ReadIteratorMakeRange() argument 242 …eadIteratorInit ( ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, … in CSRA1_ReadIteratorMakeRange() 271 bool wants_full, in CSRA1_ReadIteratorMakeReadGroup() argument 282 wants_full, in CSRA1_ReadIteratorMakeReadGroup() 477 if ( self -> wants_full ) in CSRA1_ReadIteratorNext()
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H A D | CSRA1_Read.h | 63 bool wants_full, 75 bool wants_full, 88 bool wants_full,
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H A D | NGS_ReadCollection.c | 199 …eads ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… in NGS_ReadCollection_v1_get_reads() argument 202 …ON_FAIL ( struct NGS_Read * ret = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wan… in NGS_ReadCollection_v1_get_reads() 211 …ount ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… in NGS_ReadCollection_v1_get_read_count() argument 214 …ON_FAIL ( uint64_t ret = NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_pa… in NGS_ReadCollection_v1_get_read_count() 226 …t = NGS_ReadCollectionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, … 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 | 102 bool wants_full; member 137 bool wants_full, 153 bool wants_full, 166 bool wants_full,
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H A D | SRA_Read.c | 117 self -> wants_full = true; in SRA_ReadInit() 131 bool wants_full, in SRA_ReadIteratorInit() argument 145 self -> wants_full = wants_full; in SRA_ReadIteratorInit() 556 bool wants_full, in SRA_ReadIteratorMake() argument 578 …TRY ( SRA_ReadIteratorInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_p… in SRA_ReadIteratorMake() 603 bool wants_full, in SRA_ReadIteratorMakeRange() argument 625 …TRY ( SRA_ReadIteratorInit ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_p… in SRA_ReadIteratorMakeRange() 652 bool wants_full, in SRA_ReadIteratorMakeReadGroup() argument 663 wants_full, in SRA_ReadIteratorMakeReadGroup() 710 if ( ! self -> wants_full || 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 …virtual ngs_adapt::ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool … 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 …virtual ngs_adapt::ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool … 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 …virtual ngs_adapt::ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool … 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 …ds ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 75 …nt ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 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 …ds ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 75 …nt ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 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 …ds ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 75 …nt ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_part… 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 | 356 bool wants_full = ( categories & Read :: fullyAligned ) != 0; in getReads() local 359 …NGS_Read_v1 * ret = ( * vt -> get_reads ) ( self, & err, wants_full, wants_partial, wants_unalign… in getReads() 379 bool wants_full = ( categories & Read :: fullyAligned ) != 0; in getReadCount() local 382 …uint64_t ret = ( * vt -> get_read_count ) ( self, & err, wants_full, wants_partial, wants_unalign… in getReadCount() 422 bool wants_full = ( categories & Read :: fullyAligned ) != 0; in getReadRange() local 425 …NGS_Read_v1 * ret = ( * vt -> get_read_range ) ( self, & err, first, count, wants_full, wants_par… in getReadRange()
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