Searched refs:BAM_Alignment (Results 1 – 8 of 8) sorted by relevance
30 typedef struct BAM_Alignment BAM_Alignment; typedef35 rc_t BAM_AlignmentAddRef ( const BAM_Alignment *self );36 rc_t BAM_AlignmentRelease ( const BAM_Alignment *self );42 BAM_Alignment *BAM_AlignmentCopy(const BAM_Alignment *self);60 BAM_Alignment *BAM_AlignmentDetach(const BAM_Alignment *self);164 bool BAM_AlignmentIsMapped ( const BAM_Alignment *self );330 rc_t BAM_AlignmentGetCigar ( const BAM_Alignment *self,341 rc_t BAM_AlignmentFormatSAM(const BAM_Alignment *self,438 bool BAM_AlignmentHasCGData(BAM_Alignment const *self);446 rc_t BAM_AlignmentGetCGCigar(BAM_Alignment const *self,[all …]
143 static inline int getRefSeqId(BAM_Alignment const *const self) { in getRefSeqId()147 static inline int getPosition(BAM_Alignment const *const self) { in getPosition()155 static inline int getBin(BAM_Alignment const *const self) { in getBin()159 static inline int getMapQual(BAM_Alignment const *const self) { in getMapQual()163 static inline int getCigarCount(BAM_Alignment const *const self) { in getCigarCount()167 static inline int getFlags(BAM_Alignment const *const self) { in getFlags()171 static inline unsigned getReadLen(BAM_Alignment const *const self) { in getReadLen()175 static inline int getMateRefSeqId(BAM_Alignment const *const self) { in getMateRefSeqId()179 static inline int getMatePos(BAM_Alignment const *const self) { in getMatePos()183 static inline int getInsertSize(BAM_Alignment const *const self) { in getInsertSize()[all …]
383 BAM_Alignment const *const self = ctx; in OptTag_sort()457 static char const *get_RG(BAM_Alignment const *cself) in get_RG()463 static char const *get_CS(BAM_Alignment const *cself) in get_CS()486 static char const *get_XT(BAM_Alignment const *cself) in get_XT()528 static char const *get_BX(BAM_Alignment const *cself) in get_BX()1732 BAM_Alignment temp; in BAM_AlignmentNumExtraFromData()1762 BAM_Alignment *y = self->nocopy; in BAM_FileMakeAlignment()2285 BAM_Alignment *BAM_AlignmentDetach(const BAM_Alignment *self) in BAM_AlignmentDetach()2296 return (BAM_Alignment *)self; in BAM_AlignmentDetach()2299 BAM_Alignment *BAM_AlignmentCopy(const BAM_Alignment *self) in BAM_AlignmentCopy()[all …]
52 static rc_t writeSAM(BAM_Alignment const *const rec) in writeSAM()86 BAM_Alignment const *rec = NULL; in samview()
134 struct BAM_Alignment { struct155 #define BAM_ALIGNMENT_SIZE(NUM_EXTRA) offsetof(struct BAM_Alignment, extra[NUM_EXTRA]) argument
886 static uint8_t GetMapQ(BAM_Alignment const *rec) in GetMapQ()1408 static rc_t BAM_FileReadDetached(BAM_File const *self, BAM_Alignment **rec) in BAM_FileReadDetached()1410 BAM_Alignment const *crec = NULL; in BAM_FileReadDetached()1427 BAM_Alignment *rec = NULL; in run_bamread_thread()1474 static BAM_Alignment const *getNextRecord(BAM_File const *const bam, rc_t *const rc) in getNextRecord()1487 BAM_Alignment const *rec = NULL; in getNextRecord()1517 static void getSpotGroup(BAM_Alignment const *const rec, char spotGroup[]) in getSpotGroup()1528 static char const *getLinkageGroup(BAM_Alignment const *const rec) in getLinkageGroup()1564 const BAM_Alignment *rec; in ProcessBAM()2652 BAM_AlignmentRelease((BAM_Alignment *)rr); in ProcessBAM()
29 typedef struct BAM_Alignment BAM_Alignment; typedef69 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentWhack() argument78 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentAlignmentId()88 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentReferenceSpec()101 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentMappingQuality()114 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentReferenceBases()138 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentReadGroup()154 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentReadId()190 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentClippedFragmentBases()207 BAM_Alignment *const self = (BAM_Alignment *)vp; in BAM_AlignmentClippedFragmentQualities()[all …]