/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 …t64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0; 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 …t64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0; 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 …t64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0; 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 ); 139 bool wants_unaligned ); 173 … NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_partial, bool wants_unaligned ); 176 bool wants_full, bool wants_partial, bool wants_unaligned ); 177 …t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
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H A D | CSRA1_Read.c | 114 self -> wants_unaligned = true; in CSRA1_ReadInit() 143 bool wants_unaligned ) in CSRA1_ReadIteratorInit() argument 158 self -> wants_unaligned = wants_unaligned; in CSRA1_ReadIteratorInit() 171 bool wants_unaligned ) in CSRA1_ReadIteratorMake() argument 192 …ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in CSRA1_ReadIteratorMake() 221 bool wants_unaligned ) in CSRA1_ReadIteratorMakeRange() argument 242 …ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in CSRA1_ReadIteratorMakeRange() 273 bool wants_unaligned ) in CSRA1_ReadIteratorMakeReadGroup() argument 284 wants_unaligned ) ) in CSRA1_ReadIteratorMakeReadGroup() 528 ( cat == NGS_ReadCategory_unaligned && ! self -> wants_unaligned ) ) in CSRA1_ReadIteratorNext()
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H A D | CSRA1_Read.h | 65 bool wants_unaligned ); 77 bool wants_unaligned ); 90 bool wants_unaligned );
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H A D | NGS_ReadCollection.c | 199 …ction_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollection_v1_get_reads() argument 202 …t = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wants_partial, wants_unaligned ) ) in NGS_ReadCollection_v1_get_reads() 211 …ction_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollection_v1_get_read_count() argument 214 …NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_partial, wants_unaligned ) ) in NGS_ReadCollection_v1_get_read_count() 226 …tionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, wants_unaligned ) ) 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 | 104 bool wants_unaligned; member 139 bool wants_unaligned ); 155 bool wants_unaligned ); 168 bool wants_unaligned );
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H A D | SRA_Read.c | 119 self -> wants_unaligned = true; in SRA_ReadInit() 133 bool wants_unaligned ) in SRA_ReadIteratorInit() argument 147 self -> wants_unaligned = wants_unaligned; in SRA_ReadIteratorInit() 558 bool wants_unaligned ) in SRA_ReadIteratorMake() argument 578 … ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in SRA_ReadIteratorMake() 605 bool wants_unaligned ) in SRA_ReadIteratorMakeRange() argument 625 … ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in SRA_ReadIteratorMakeRange() 654 bool wants_unaligned ) in SRA_ReadIteratorMakeReadGroup() argument 665 wants_unaligned ) ) in SRA_ReadIteratorMakeReadGroup() 712 ! self -> wants_unaligned ) in SRA_ReadIteratorNext() [all …]
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H A D | SRA_DB_ReadCollection.c | 238 bool wants_full, bool wants_partial, bool wants_unaligned ) in SRA_DB_ReadCollectionGetReads() argument 242 if ( ! wants_unaligned ) in SRA_DB_ReadCollectionGetReads() 250 …torMake ( ctx, curs, self -> run_name, /*wants_full, wants_partial*/ true, true, wants_unaligned ); in SRA_DB_ReadCollectionGetReads() 293 …RA_DB_ReadCollection * self, ctx_t ctx, bool wants_full, bool wants_partial, bool wants_unaligned ) in SRA_DB_ReadCollectionGetReadCount() argument 297 if ( ! wants_unaligned ) in SRA_DB_ReadCollectionGetReadCount() 310 bool wants_full, bool wants_partial, bool wants_unaligned ) in SRA_DB_ReadCollectionGetReadRange() argument 316 … curs, self -> run_name, first, count, /*wants_full, wants_partial*/ true, true, wants_unaligned ); in SRA_DB_ReadCollectionGetReadRange()
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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 ); 139 bool wants_unaligned ); 173 … NGS_READCOLLECTION * self, ctx_t ctx, bool wants_full, bool wants_partial, bool wants_unaligned ); 176 bool wants_full, bool wants_partial, bool wants_unaligned ); 177 …t ctx, uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
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H A D | CSRA1_Read.c | 114 self -> wants_unaligned = true; in CSRA1_ReadInit() 143 bool wants_unaligned ) in CSRA1_ReadIteratorInit() argument 158 self -> wants_unaligned = wants_unaligned; in CSRA1_ReadIteratorInit() 171 bool wants_unaligned ) in CSRA1_ReadIteratorMake() argument 192 …ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in CSRA1_ReadIteratorMake() 221 bool wants_unaligned ) in CSRA1_ReadIteratorMakeRange() argument 242 …ctx, cref, "CSRA1_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in CSRA1_ReadIteratorMakeRange() 273 bool wants_unaligned ) in CSRA1_ReadIteratorMakeReadGroup() argument 284 wants_unaligned ) ) in CSRA1_ReadIteratorMakeReadGroup() 528 ( cat == NGS_ReadCategory_unaligned && ! self -> wants_unaligned ) ) in CSRA1_ReadIteratorNext()
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H A D | CSRA1_Read.h | 65 bool wants_unaligned ); 77 bool wants_unaligned ); 90 bool wants_unaligned );
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H A D | NGS_ReadCollection.c | 199 …ction_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollection_v1_get_reads() argument 202 …t = NGS_ReadCollectionGetReads ( Self ( self ), ctx, wants_full, wants_partial, wants_unaligned ) ) in NGS_ReadCollection_v1_get_reads() 211 …ction_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ) in NGS_ReadCollection_v1_get_read_count() argument 214 …NGS_ReadCollectionGetReadCount ( Self ( self ), ctx, wants_full, wants_partial, wants_unaligned ) ) in NGS_ReadCollection_v1_get_read_count() 226 …tionGetReadRange ( Self ( self ), ctx, first, count, wants_full, wants_partial, wants_unaligned ) ) 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 | 104 bool wants_unaligned; member 139 bool wants_unaligned ); 155 bool wants_unaligned ); 168 bool wants_unaligned );
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H A D | SRA_Read.c | 119 self -> wants_unaligned = true; in SRA_ReadInit() 133 bool wants_unaligned ) in SRA_ReadIteratorInit() argument 147 self -> wants_unaligned = wants_unaligned; in SRA_ReadIteratorInit() 558 bool wants_unaligned ) in SRA_ReadIteratorMake() argument 578 … ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in SRA_ReadIteratorMake() 605 bool wants_unaligned ) in SRA_ReadIteratorMakeRange() argument 625 … ( ctx, ref, "NGS_ReadIterator", instname, run_name, wants_full, wants_partial, wants_unaligned ) ) in SRA_ReadIteratorMakeRange() 654 bool wants_unaligned ) in SRA_ReadIteratorMakeReadGroup() argument 665 wants_unaligned ) ) in SRA_ReadIteratorMakeReadGroup() 712 ! self -> wants_unaligned ) 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 … ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReads() 117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() 122 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadRange()
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/test/test_engine/ |
H A D | ReadCollectionItf.hpp | 112 … ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReads() 117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() 122 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadRange()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/test/test_engine/ |
H A D | ReadCollectionItf.hpp | 112 … ngs_adapt::ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReads() 117 … virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadCount() 122 … uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const in getReadRange()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/itf/ |
H A D | ReadCollectionItf.h | 74 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 75 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 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 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 75 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 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 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 75 …tion_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned ); 77 uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
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