1 #ifndef theplu_yat_omic_bam_read
2 #define theplu_yat_omic_bam_read
25 #include "config_bam.h"
26 #include YAT_BAM_HEADER
27 #include YAT_SAM_HEADER
29 #include "yat/utility/Aligner.h"
31 #include "yat/utility/Cigar.h"
84 const uint8_t*
aux(
void)
const;
97 const uint8_t*
aux(
const char tag[2])
const;
111 void aux_append(
const char tag[2],
char type,
int len, uint8_t* data);
120 void aux_del(
const char tag[2]);
134 const bam1_core_t&
core(
void)
const;
141 bam1_core_t&
core(
void);
149 const uint32_t*
cigar(
void)
const;
154 uint32_t
cigar(
size_t i)
const;
179 void cigar(
const std::vector<uint32_t>& c) YAT_DEPRECATE;
198 int32_t
end(
void)
const;
207 uint16_t
flag(
void)
const;
212 int32_t
mpos(
void)
const;
217 int32_t
mtid(
void)
const;
224 const char*
name(
void)
const;
231 void name(
const std::string& n);
236 int32_t
pos(
void)
const;
241 uint8_t
qual(
size_t i)
const;
251 void qual(
size_t i, uint8_t q);
265 uint8_t
sequence(
size_t index)
const;
283 void sequence(
const std::string& seq,
const std::vector<uint8_t>& qual);
300 int32_t
tid(
void)
const;
311 uint32_t calend(
const bam1_core_t *c,
const uint32_t *cigar)
const;
332 bool soft_clipped(
const BamRead& bam);
342 uint32_t left_soft_clipped(
const BamRead& bam);
352 uint32_t right_soft_clipped(
const BamRead& bam);
374 :
public std::binary_function<const BamRead&, const BamRead&, bool>
395 :
public std::binary_function<const BamRead&, const BamRead&, bool>
void aux_del(const char tag[2])
remove a tag in aux field
virtual ~BamRead(void)
Destructor.
uint32_t sequence_length(void) const
int32_t tid(void) const
chromosome ID
BamRead(void)
default constructor
bool operator()(const BamRead &lhs, const BamRead &rhs) const
bool operator()(const BamRead &lhs, const BamRead &rhs) const
int32_t end(void) const
rightmost coordinate
const char * name(void) const
const bam1_core_t & core(void) const
access core data struct
Class holding a bam query.
Definition: BamRead.h:53
uint32_t cigar_op(size_t i) const
const BamRead & operator=(const BamRead &rhs)
assignment operator
Definition: BamRead.h:373
int32_t mtid(void) const
Chromosome ID for mate.
std::string sequence(void) const
void aux_append(const char tag[2], char type, int len, uint8_t *data)
append a new tag to aux field
const uint8_t * aux(void) const
Compact Idiosyncratic Gapped Alignment Report.
Definition: Aligner.h:177
Definition: BamFile.h:176
int32_t mpos(void) const
leftmost position for mate
Definition: BamRead.h:394
Definition: BamFile.h:105
void swap(BamRead &other)
uint32_t cigar_oplen(size_t i) const
class to iterate through a InBamFile
Definition: BamReadIterator.h:60
uint16_t flag(void) const
bitwise flag
uint8_t qual(size_t i) const
int32_t pos(void) const
0-based laftmost coordinate
const uint32_t * cigar(void) const
access CIGAR array
std::string cigar_str(void) const