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Searched refs:wants_unaligned (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 …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 );
/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 …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 );
/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 …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 );
/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 );
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 );
H A DCSRA1_Read.c114 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()
H A DCSRA1_Read.h65 bool wants_unaligned );
77 bool wants_unaligned );
90 bool wants_unaligned );
H A DNGS_ReadCollection.c199 …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 …]
H A DSRA_Read.h104 bool wants_unaligned; member
139 bool wants_unaligned );
155 bool wants_unaligned );
168 bool wants_unaligned );
H A DSRA_Read.c119 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 …]
H A DSRA_DB_ReadCollection.c238 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()
/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 );
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 );
H A DCSRA1_Read.c114 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()
H A DCSRA1_Read.h65 bool wants_unaligned );
77 bool wants_unaligned );
90 bool wants_unaligned );
H A DNGS_ReadCollection.c199 …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 …]
H A DSRA_Read.h104 bool wants_unaligned; member
139 bool wants_unaligned );
155 bool wants_unaligned );
168 bool wants_unaligned );
H A DSRA_Read.c119 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 …]
/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 … 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()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/test/test_engine/
H A DReadCollectionItf.hpp112 … 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()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/test/test_engine/
H A DReadCollectionItf.hpp112 … 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()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …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 );
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …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 );
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/itf/
H A DReadCollectionItf.h74 …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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