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#ifndef HTSLIB_UTIL_H
#define HTSLIB_UTIL_H
#include "htslib/sam.h"
#include "htslib/vcf.h"
#include "htslib/khash.h"
int hts_useek(htsFile *fp, long uoffset, int where);
long hts_utell(htsFile *fp);
int hts_set_verbosity(int verbosity);
int hts_get_verbosity();
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
typedef khash_t(vdict) vdict_t;
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
typedef khash_t(s2i) s2i_t;
//////////////////////////////////////////////////////////////////
/*! set pysam standard error to point to file descriptor
Setting the stderr will close the previous stderr.
*/
// FILE * pysam_set_stderr(int fd);
//////////////////////////////////////////////////////////////////
/*! set pysam standard error to /dev/null.
Unsetting the stderr will close the previous stderr.
*/
// void pysam_unset_stderr();
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
// various helper functions
//
/*!
@abstract Update the variable length data within a bam1_t entry
Old data is deleted and the data within b are re-arranged to
make place for new data.
@discussion Returns b
@param b bam1_t data
@param nbytes_old size of old data
@param nbytes_new size of new data
@param pos position of data
*/
bam1_t * pysam_bam_update(bam1_t * b,
const size_t nbytes_old,
const size_t nbytes_new,
uint8_t * pos);
// translate a nucleotide character to binary code
unsigned char pysam_translate_sequence(const unsigned char s);
// return byte size of type
int aux_type2size(uint8_t type);
//-------------------------------------------------------
// Wrapping accessor macros in sam.h
static inline int pysam_bam_is_rev(bam1_t * b) {
return bam_is_rev(b);};
static inline int pysam_bam_is_mrev(bam1_t * b) {
return bam_is_mrev(b);}
static inline char * pysam_bam_get_qname(bam1_t * b) {
return bam_get_qname(b);}
static inline uint32_t * pysam_bam_get_cigar(bam1_t * b) {
return bam_get_cigar(b);}
static inline uint8_t * pysam_bam_get_seq(bam1_t * b) {
return bam_get_seq(b);}
static inline uint8_t * pysam_bam_get_qual(bam1_t * b) {
return bam_get_qual(b);}
static inline uint8_t * pysam_bam_get_aux(bam1_t * b) {
return bam_get_aux(b);}
static inline int pysam_bam_get_l_aux(bam1_t * b) {
return bam_get_l_aux(b); }
static inline char pysam_bam_seqi(uint8_t * s, int i) {
return bam_seqi(s,i);}
// Wrapping bit field access in bam1_core_t
// bit fields not supported in cython and due
// to endian-ness it is not clear which part
// of the bit-field is in the higher or lower bytes.
static inline uint16_t pysam_get_bin(bam1_t * b) {
return b->core.bin;}
static inline uint8_t pysam_get_qual(bam1_t * b) {
return b->core.qual;}
static inline uint8_t pysam_get_l_qname(bam1_t * b) {
return b->core.l_qname;}
static inline uint16_t pysam_get_flag(bam1_t * b) {
return b->core.flag;}
static inline uint16_t pysam_get_n_cigar(bam1_t * b) {
return b->core.n_cigar;}
static inline void pysam_set_bin(bam1_t * b, uint16_t v) {
b->core.bin=v;}
static inline void pysam_set_qual(bam1_t * b, uint8_t v) {
b->core.qual=v;}
static inline void pysam_set_l_qname(bam1_t * b, uint8_t v) {
b->core.l_qname=v;}
static inline void pysam_set_flag(bam1_t * b, uint16_t v) {
b->core.flag=v;}
static inline void pysam_set_n_cigar(bam1_t * b, uint16_t v) {
b->core.n_cigar=v;}
static inline void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) {
if (v)
b->core.flag |= flag;
else
b->core.flag &= ~flag;
}
#endif
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