Imported Upstream version 0.3

[pysam.git] / pysam / pysam_util.h

diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
index ff5d569ee24019d8abeb0bb72b2decef7a0d707a..bfbd6dd0016b73ad94a9ad2d34c5811f969a0d82 100644 (file)
--- a/pysam/pysam_util.h
+++ b/pysam/pysam_util.h
@@ -1,75 +1,22 @@
 #ifndef PYSAM_UTIL_H
 #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);
-
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////
 // 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