Elementolab/BAM C Library

From Icbwiki

A few useful pointers:

http://samtools.sourceforge.net/samtools/sam/Functions/Functions.html
http://samtools.sourceforge.net/samtools/bam/index.html
http://samtools.sourcearchive.com/documentation/0.1.5c/bam_8h-source.html
http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ
http://code.google.com/r/jeffhsu3-pysamclone/source/browse/pysam/bam.c?r=405adaf9b1241494b1768f4077c96fa639829f4a&spec=svnd1f2a0c9425334bef13046aec39e7e02dac18399

Some code:

#include <stdio.h>
#include "lib/third_party/samtools/sam.h"
#include "lib/third_party/samtools/bam.h"

#define bam1_unmapped(b) (((b)->core.flag & BAM_FUNMAP) != 0)

int main(int argc, char *argv[])
{
  int i;
  samfile_t* in;
  if (argc == 1) {
   fprintf(stderr, "Usage: calDepth <in.bam> [region]\n");
   return 1;
  }
 
  in = samopen(argv[1], "rb", 0);
  if (in == 0) {
    fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
    return 1;
  }

  bam1_t* b = bam_init1();
  int ret;
  while ((ret = samread(in, b)) >= 0) {

    printf("%d(%d)\t", b->core.flag, BAM_FUNMAP);

    if (bam1_unmapped(b)) {
      printf("Unmapped:\t");
    } else {
      printf("Mapped:\t");
    }

    printf("%s", in->header->target_name[b->core.tid]);
    printf("\t%s", bam1_qname(b));
    printf("\t%d", b->core.pos);
    char* c = (char*)(bam1_aux(b));
    c[4] = '\0';
 

    //for (i=0; il_aux; i++) {
   //  if (c[i] != '\n') {
   //printf("'%c'\n", c[i]);
   //  }
   //}

   printf("\t%s", c);
   printf("\t%d\n", bam1_strand(b));
 }
	
 
 samclose(in);
 return 0;
}