X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fpysam_util.h;h=89e381bbd8fee3762d56a1d7dad14b9c44f6b8a2;hp=ff5d569ee24019d8abeb0bb72b2decef7a0d707a;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=aa8ecff068edbb09a03bd874fce716e93e22e53c

diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
index ff5d569..89e381b 100644
--- a/pysam/pysam_util.h
+++ b/pysam/pysam_util.h
@@ -2,74 +2,25 @@
 #define PYSAM_UTIL_H
 
 //////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////
-// code for iterator
-
-/*! @typedef
-  @Structure for holding current state (current alignment etc.) for iterating through
-  alignments overlapping a specified region.
-  @field  b           pointer to the current alignment
-  @field  off         pointer to an array of chunk loci (each with beg/end positions)
-  @field  n_off       The number of chunks
-  @field  curr_off    The current file positon
-  @field  curr_chunk  The item in a list of chunk
-  @discussion See also bam_fetch_iterate
-*/
-struct __bam_fetch_iterator_t;
-typedef struct __bam_fetch_iterator_t bam_fetch_iterator_t;
-	
-/*!
-  @abstract Retrieve the alignments that are overlapped with the
-  specified region.
-  
-  @discussion Returns iterator object to retrieve successive alignments ordered by
-  start position. 
-  @param  fp    BAM file handler
-  @param  idx   pointer to the alignment index
-  @param  tid   chromosome ID as is defined in the header
-  @param  beg   start coordinate, 0-based
-  @param  end   end coordinate, 0-based
-*/
-bam_fetch_iterator_t * bam_init_fetch_iterator(bamFile fp, const bam_index_t *idx, int tid, int beg, int end);
-
-
-/*!
-  @abstract Iterates through alignments overlapped the specified region.
-  @discussion Returns pointer to successive alignments ordered by start position.
-  Returns null pointer to signal the end of the iteration.
-  The alignment data is nested within the iterator to avoid unnecessary allocations.
-*/
-bam1_t * bam_fetch_iterate(bam_fetch_iterator_t *iter);
-
-bam_fetch_iterator_t* bam_init_fetchall_iterator(bamFile fp, const bam_index_t *idx);
-bam1_t * bam_fetchall_iterate(bam_fetch_iterator_t *iter);
+// set pysam standard error to point to stream
+FILE * pysam_set_stderr( FILE * f );
 
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
 // various helper functions
+//
+// fill pileup buffer for next position.
 
-int pysam_bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf, int cont);
-
-// accessor functions - necessary as bam_plbuf_t is hidden
-// among the implementation
-int pysam_get_pos( const bam_plbuf_t *buf);
-int pysam_get_tid( const bam_plbuf_t *buf);
-bam_pileup1_t * pysam_get_pileup( const bam_plbuf_t *buf);
+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[] );
 
-// stand-in for macro - not wrappable in pyrex
-void pysam_bam_destroy1( bam1_t * b );
-
-// stand-in for other samtools macros
-uint32_t * pysam_bam1_cigar( const bam1_t * b);
-char * pysam_bam1_qname( const bam1_t * b);
-uint8_t * pysam_bam1_seq( const bam1_t * b);
-uint8_t * pysam_bam1_qual( const bam1_t * b);
-uint8_t * pysam_bam1_aux( const bam1_t * b);
-
 /*!
   @abstract Update the variable length data within a bam1_t entry
 
@@ -91,5 +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