Imported Upstream version 0.6

[pysam.git] / pysam / pysam_util.h

diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
index bfbd6dd0016b73ad94a9ad2d34c5811f969a0d82..c6184eb756cca0241dc06449b829f4198ebef02a 100644 (file)
--- a/pysam/pysam_util.h
+++ b/pysam/pysam_util.h
@@ -1,6 +1,10 @@
 #ifndef PYSAM_UTIL_H
 #define PYSAM_UTIL_H
 
+//////////////////////////////////////////////////////////////////
+// set pysam standard error to point to stream
+FILE * pysam_set_stderr( FILE * f );
+
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
@@ -38,5 +42,24 @@ bam1_t * pysam_bam_update( bam1_t * b,
 // 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 ); */
+
 
 #endif