#ifndef PYSAM_UTIL_H
#define PYSAM_UTIL_H
+//////////////////////////////////////////////////////////////////
+/*! 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();
+
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
// 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