Home
last modified time | relevance | path

Searched refs:NGS_ReadCollection (Results 1 – 25 of 44) sorted by relevance

12

/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/
H A DNGS_ReadCollection.h30 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 …]
H A DNGS_ReadCollection.c61 ( ( 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 …]
H A DBAM_Alignment.h45 struct NGS_ReadCollection;
50 struct BAM_Record *(*provider)(struct NGS_ReadCollection *, ctx_t),
51 struct NGS_ReadCollection *,
H A DCSRA1_Reference.h42 struct NGS_ReadCollection;
68 struct NGS_ReadCollection * coll,
75 struct NGS_ReadCollection * coll,
H A DCSRA1_ReferenceWindow.h44 struct NGS_ReadCollection;
47 struct NGS_ReadCollection * coll,
H A DNGS_Reference.h48 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 );
H A DBAM_ReadCollection.c122 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 …]
H A DBAM_Alignment.c59 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()
H A DCSRA1_ReadCollection.h46 struct NGS_ReadCollection * CSRA1_ReadCollectionToNGS_ReadCollection ( struct CSRA1_ReadCollection …
H A DNCBI-NGS.c46 ON_FAIL ( NGS_ReadCollection * ret = NGS_ReadCollectionMake ( ctx, spec ) ) in NCBI_NGS_OpenReadCollection()
H A DMakefile101 NGS_ReadCollection \
H A DSRA_DB_ReadCollection.c70 NGS_ReadCollection dad;
400 NGS_ReadCollection * NGS_ReadCollectionMakeVDatabase ( ctx_t ctx, const VDatabase *db, const char *… in NGS_ReadCollectionMakeVDatabase()
H A DSRA_ReadCollection.c65 NGS_ReadCollection dad;
368 NGS_ReadCollection * NGS_ReadCollectionMakeVTable ( ctx_t ctx, const VTable *tbl, const char * spec… in NGS_ReadCollectionMakeVTable()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/
H A DNGS_ReadCollection.h30 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 …]
H A DNGS_ReadCollection.c61 ( ( 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 …]
H A DBAM_Alignment.h45 struct NGS_ReadCollection;
50 struct BAM_Record *(*provider)(struct NGS_ReadCollection *, ctx_t),
51 struct NGS_ReadCollection *,
H A DCSRA1_Reference.h42 struct NGS_ReadCollection;
68 struct NGS_ReadCollection * coll,
75 struct NGS_ReadCollection * coll,
H A DCSRA1_ReferenceWindow.h44 struct NGS_ReadCollection;
47 struct NGS_ReadCollection * coll,
H A DNGS_Reference.h48 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 );
H A DBAM_ReadCollection.c122 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 …]
H A DBAM_Alignment.c59 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()
H A DCSRA1_ReadCollection.h46 struct NGS_ReadCollection * CSRA1_ReadCollectionToNGS_ReadCollection ( struct CSRA1_ReadCollection …
H A DNCBI-NGS.c46 ON_FAIL ( NGS_ReadCollection * ret = NGS_ReadCollectionMake ( ctx, spec ) ) in NCBI_NGS_OpenReadCollection()
H A DMakefile101 NGS_ReadCollection \
H A DSRA_DB_ReadCollection.c70 NGS_ReadCollection dad;
400 NGS_ReadCollection * NGS_ReadCollectionMakeVDatabase ( ctx_t ctx, const VDatabase *db, const char *… in NGS_ReadCollectionMakeVDatabase()

12