/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
H A D | NGS_ReadCollection.h | 30 typedef struct NGS_ReadCollection NGS_ReadCollection; typedef 32 #define NGS_READCOLLECTION NGS_ReadCollection 82 NGS_ReadCollection * NGS_ReadCollectionMake ( ctx_t ctx, const char * spec ); 95 struct NGS_String * NGS_ReadCollectionGetName ( NGS_ReadCollection * self, ctx_t ctx ); 114 struct NGS_Alignment * NGS_ReadCollectionGetAlignments ( NGS_ReadCollection * self, ctx_t ctx, 118 uint64_t NGS_ReadCollectionGetAlignmentCount ( NGS_ReadCollection * self, ctx_t ctx, 127 struct NGS_Read * NGS_ReadCollectionGetReads ( NGS_ReadCollection * self, ctx_t ctx, 130 uint64_t NGS_ReadCollectionGetReadCount ( NGS_ReadCollection * self, ctx_t ctx, 133 struct NGS_Read * NGS_ReadCollectionGetReadRange ( NGS_ReadCollection * self, 152 struct NGS_ReadCollection struct [all …]
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H A D | NGS_ReadCollection.c | 61 ( ( NGS_ReadCollection* ) ( obj ) ) 277 struct NGS_String * NGS_ReadCollectionGetName ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetName() 295 struct NGS_ReadGroup * NGS_ReadCollectionGetReadGroups ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetReadGroups() 310 bool NGS_ReadCollectionHasReadGroup ( NGS_ReadCollection * self, ctx_t ctx, const char * spec ) in NGS_ReadCollectionHasReadGroup() 345 struct NGS_Reference * NGS_ReadCollectionGetReferences ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetReferences() 360 bool NGS_ReadCollectionHasReference ( NGS_ReadCollection * self, ctx_t ctx, const char * spec ) in NGS_ReadCollectionHasReference() 399 struct NGS_Alignment * NGS_ReadCollectionGetAlignments ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetAlignments() 465 struct NGS_Read * NGS_ReadCollectionGetReads ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetReads() 498 uint64_t NGS_ReadCollectionGetReadCount ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetReadCount() 565 NGS_ReadCollection * NGS_ReadCollectionMake ( ctx_t ctx, const char * spec ) in NGS_ReadCollectionMake() [all …]
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H A D | BAM_Alignment.h | 45 struct NGS_ReadCollection; 50 struct BAM_Record *(*provider)(struct NGS_ReadCollection *, ctx_t), 51 struct NGS_ReadCollection *,
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H A D | CSRA1_Reference.h | 42 struct NGS_ReadCollection; 68 struct NGS_ReadCollection * coll, 75 struct NGS_ReadCollection * coll,
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H A D | CSRA1_ReferenceWindow.h | 44 struct NGS_ReadCollection; 47 struct NGS_ReadCollection * coll,
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H A D | NGS_Reference.h | 48 struct NGS_ReadCollection; 172 struct NGS_ReadCollection * coll; 208 struct NGS_ReadCollection * coll ); 217 struct NGS_Reference * NGS_ReferenceMakeNull ( ctx_t ctx, struct NGS_ReadCollection * coll );
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H A D | BAM_ReadCollection.c | 122 NGS_ReadCollection dad; 182 static NGS_String * BAM_ReadCollectionName(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionName() 189 static NGS_ReadGroup * BAM_ReadCollectionReadGroups(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReadGroups() 196 static NGS_ReadGroup * BAM_ReadCollectionReadGroup(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionReadGroup() 422 static NGS_Reference * BAM_ReadCollectionReferences(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReferences() 447 static NGS_Reference * BAM_ReadCollectionReference(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionReference() 481 static NGS_Alignment * BAM_ReadCollectionAlignment(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionAlignment() 509 static struct NGS_Read * BAM_ReadCollectionRead(NGS_ReadCollection *const vp, ctx_t ctx, char const… in BAM_ReadCollectionRead() 516 static uint64_t BAM_ReadCollectionReadCount(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReadCount() 1488 NGS_ReadCollection * NGS_ReadCollectionMakeBAM(ctx_t ctx, char const path[]) in NGS_ReadCollectionMakeBAM() [all …]
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H A D | BAM_Alignment.c | 59 struct BAM_Record *(*provider_f)(struct NGS_ReadCollection *, ctx_t); 60 struct NGS_ReadCollection *provider; 627 … struct BAM_Record *(*const provider_f)(struct NGS_ReadCollection *, ctx_t), in BAM_AlignmentInit() argument 628 struct NGS_ReadCollection *const provider) in BAM_AlignmentInit() 637 … struct BAM_Record *(*const provider_f)(struct NGS_ReadCollection *, ctx_t), in BAM_AlignmentMake() argument 638 struct NGS_ReadCollection *const provider, in BAM_AlignmentMake()
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H A D | CSRA1_ReadCollection.h | 46 struct NGS_ReadCollection * CSRA1_ReadCollectionToNGS_ReadCollection ( struct CSRA1_ReadCollection …
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H A D | NCBI-NGS.c | 46 ON_FAIL ( NGS_ReadCollection * ret = NGS_ReadCollectionMake ( ctx, spec ) ) in NCBI_NGS_OpenReadCollection()
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H A D | Makefile | 101 NGS_ReadCollection \
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H A D | SRA_DB_ReadCollection.c | 70 NGS_ReadCollection dad; 400 NGS_ReadCollection * NGS_ReadCollectionMakeVDatabase ( ctx_t ctx, const VDatabase *db, const char *… in NGS_ReadCollectionMakeVDatabase()
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H A D | SRA_ReadCollection.c | 65 NGS_ReadCollection dad; 368 NGS_ReadCollection * NGS_ReadCollectionMakeVTable ( ctx_t ctx, const VTable *tbl, const char * spec… in NGS_ReadCollectionMakeVTable()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
H A D | NGS_ReadCollection.h | 30 typedef struct NGS_ReadCollection NGS_ReadCollection; typedef 32 #define NGS_READCOLLECTION NGS_ReadCollection 82 NGS_ReadCollection * NGS_ReadCollectionMake ( ctx_t ctx, const char * spec ); 95 struct NGS_String * NGS_ReadCollectionGetName ( NGS_ReadCollection * self, ctx_t ctx ); 114 struct NGS_Alignment * NGS_ReadCollectionGetAlignments ( NGS_ReadCollection * self, ctx_t ctx, 118 uint64_t NGS_ReadCollectionGetAlignmentCount ( NGS_ReadCollection * self, ctx_t ctx, 127 struct NGS_Read * NGS_ReadCollectionGetReads ( NGS_ReadCollection * self, ctx_t ctx, 130 uint64_t NGS_ReadCollectionGetReadCount ( NGS_ReadCollection * self, ctx_t ctx, 133 struct NGS_Read * NGS_ReadCollectionGetReadRange ( NGS_ReadCollection * self, 152 struct NGS_ReadCollection struct [all …]
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H A D | NGS_ReadCollection.c | 61 ( ( NGS_ReadCollection* ) ( obj ) ) 277 struct NGS_String * NGS_ReadCollectionGetName ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetName() 295 struct NGS_ReadGroup * NGS_ReadCollectionGetReadGroups ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetReadGroups() 310 bool NGS_ReadCollectionHasReadGroup ( NGS_ReadCollection * self, ctx_t ctx, const char * spec ) in NGS_ReadCollectionHasReadGroup() 345 struct NGS_Reference * NGS_ReadCollectionGetReferences ( NGS_ReadCollection * self, ctx_t ctx ) in NGS_ReadCollectionGetReferences() 360 bool NGS_ReadCollectionHasReference ( NGS_ReadCollection * self, ctx_t ctx, const char * spec ) in NGS_ReadCollectionHasReference() 399 struct NGS_Alignment * NGS_ReadCollectionGetAlignments ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetAlignments() 465 struct NGS_Read * NGS_ReadCollectionGetReads ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetReads() 498 uint64_t NGS_ReadCollectionGetReadCount ( NGS_ReadCollection * self, ctx_t ctx, in NGS_ReadCollectionGetReadCount() 565 NGS_ReadCollection * NGS_ReadCollectionMake ( ctx_t ctx, const char * spec ) in NGS_ReadCollectionMake() [all …]
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H A D | BAM_Alignment.h | 45 struct NGS_ReadCollection; 50 struct BAM_Record *(*provider)(struct NGS_ReadCollection *, ctx_t), 51 struct NGS_ReadCollection *,
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H A D | CSRA1_Reference.h | 42 struct NGS_ReadCollection; 68 struct NGS_ReadCollection * coll, 75 struct NGS_ReadCollection * coll,
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H A D | CSRA1_ReferenceWindow.h | 44 struct NGS_ReadCollection; 47 struct NGS_ReadCollection * coll,
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H A D | NGS_Reference.h | 48 struct NGS_ReadCollection; 172 struct NGS_ReadCollection * coll; 208 struct NGS_ReadCollection * coll ); 217 struct NGS_Reference * NGS_ReferenceMakeNull ( ctx_t ctx, struct NGS_ReadCollection * coll );
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H A D | BAM_ReadCollection.c | 122 NGS_ReadCollection dad; 182 static NGS_String * BAM_ReadCollectionName(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionName() 189 static NGS_ReadGroup * BAM_ReadCollectionReadGroups(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReadGroups() 196 static NGS_ReadGroup * BAM_ReadCollectionReadGroup(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionReadGroup() 422 static NGS_Reference * BAM_ReadCollectionReferences(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReferences() 447 static NGS_Reference * BAM_ReadCollectionReference(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionReference() 481 static NGS_Alignment * BAM_ReadCollectionAlignment(NGS_ReadCollection *const vp, ctx_t ctx, char co… in BAM_ReadCollectionAlignment() 509 static struct NGS_Read * BAM_ReadCollectionRead(NGS_ReadCollection *const vp, ctx_t ctx, char const… in BAM_ReadCollectionRead() 516 static uint64_t BAM_ReadCollectionReadCount(NGS_ReadCollection *const vp, ctx_t ctx) { in BAM_ReadCollectionReadCount() 1488 NGS_ReadCollection * NGS_ReadCollectionMakeBAM(ctx_t ctx, char const path[]) in NGS_ReadCollectionMakeBAM() [all …]
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H A D | BAM_Alignment.c | 59 struct BAM_Record *(*provider_f)(struct NGS_ReadCollection *, ctx_t); 60 struct NGS_ReadCollection *provider; 627 … struct BAM_Record *(*const provider_f)(struct NGS_ReadCollection *, ctx_t), in BAM_AlignmentInit() argument 628 struct NGS_ReadCollection *const provider) in BAM_AlignmentInit() 637 … struct BAM_Record *(*const provider_f)(struct NGS_ReadCollection *, ctx_t), in BAM_AlignmentMake() argument 638 struct NGS_ReadCollection *const provider, in BAM_AlignmentMake()
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H A D | CSRA1_ReadCollection.h | 46 struct NGS_ReadCollection * CSRA1_ReadCollectionToNGS_ReadCollection ( struct CSRA1_ReadCollection …
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H A D | NCBI-NGS.c | 46 ON_FAIL ( NGS_ReadCollection * ret = NGS_ReadCollectionMake ( ctx, spec ) ) in NCBI_NGS_OpenReadCollection()
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H A D | Makefile | 101 NGS_ReadCollection \
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H A D | SRA_DB_ReadCollection.c | 70 NGS_ReadCollection dad; 400 NGS_ReadCollection * NGS_ReadCollectionMakeVDatabase ( ctx_t ctx, const VDatabase *db, const char *… in NGS_ReadCollectionMakeVDatabase()
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