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#ifndef PYSAM_UTIL_H
#define PYSAM_UTIL_H
#include "kseq.h"
// #######################################################
// fastq parsing
KSEQ_INIT(gzFile, gzread)
//////////////////////////////////////////////////////////////////
/*! 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
//
// fill pileup buffer for next position.
int pysam_pileup_next(const bam1_t *b,
bam_plbuf_t *buf,
bam_pileup1_t ** plp,
int * tid,
int * pos,
int * n_plp);
int pysam_dispatch(int argc, char *argv[] );
/*!
@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 );
// defined in bam_import.c
extern unsigned char bam_nt16_table[256];
// translate a reference string *s* to a tid
int pysam_reference2tid( bam_header_t *header, const char * s );
// return number of mapped reads for tid
uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid );
// return number of unmapped reads for tid
uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid );
// debugging functions
/* #include "glf.h" */
/* uint32_t pysam_glf_depth( glf1_t * g); */
/* #include "bam_maqcns.h" */
/* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ); */
// return size of auxilliary type
// int bam_aux_type2size(int x);
#endif
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