Imported Upstream version 0.5

[pysam.git] / pysam / pysam_util.h

diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
index bfbd6dd0016b73ad94a9ad2d34c5811f969a0d82..89e381bbd8fee3762d56a1d7dad14b9c44f6b8a2 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 +42,18 @@ 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 );
+
+// 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