Created
December 10, 2010 10:25
-
-
Save lindenb/736059 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
/* | |
gcc -m64 -I package/sam/samtools-0.1.7a -L package/sam/samtools-0.1.7a jeter.c -lbam -lz | |
*/ | |
#include <stdlib.h> | |
#include <stdio.h> | |
#include <assert.h> | |
#include "bam.h" | |
#include "sam.h" | |
int main(int argc, char *argv[]) { | |
samfile_t *fp_in = NULL; | |
bam1_t *b=NULL; | |
if(argc!=2) return EXIT_FAILURE; | |
fp_in = samopen(argv[1], "rb", 0); | |
if(NULL == fp_in) | |
{ | |
fprintf(stderr,"Could not open file\n"); | |
return EXIT_FAILURE; | |
} | |
b = bam_init1(); | |
int pos=0; | |
int lastpos=0; | |
while(samread(fp_in, b) > 0) | |
{ | |
lastpos = pos; | |
pos = b->core.pos; | |
printf("tid : %d\n",b->core.tid); | |
if(b->core.tid>=0) | |
{ | |
printf("seqname: %s\n", fp_in->header->target_name[b->core.tid]); | |
printf("seqlength: %d\n", fp_in->header->target_len[b->core.tid]); | |
} | |
printf("pos : %d\n",b->core.pos); | |
char *name = bam1_qname(b); | |
unsigned char *qual = bam1_qual(b); | |
uint32_t* cigar= bam1_cigar(b); | |
int n=0; | |
char *qseq = (char *) malloc(b->core.l_qseq+1); | |
unsigned char *s = bam1_seq(b); | |
for(n=0;n<(b->core.l_qseq);n++) { | |
int v = bam1_seqi(s,n); | |
qseq[n] = bam_nt16_rev_table[v]; | |
} | |
qseq[n] = 0; | |
int cigar_leng=bam_cigar2qlen(&(b->core),cigar); | |
printf("name : %s\n",name); | |
printf("qseq : %s\n",qseq); | |
printf("cigar-size: %d\n",cigar_leng); | |
printf("cigar:"); | |
int k; | |
for( k=0;k< b->core.n_cigar;++k) | |
{ | |
int cop =cigar[k] & BAM_CIGAR_MASK; // operation | |
int cl = cigar[k] >> BAM_CIGAR_SHIFT; // length | |
switch(cop) | |
{ | |
case BAM_CMATCH: printf("M");break; | |
case BAM_CINS: printf("I");break; | |
case BAM_CDEL: printf("D");break; | |
case BAM_CREF_SKIP: printf("N"); break; | |
case BAM_CSOFT_CLIP: printf("S");break; | |
case BAM_CHARD_CLIP: printf("R");break; | |
case BAM_CPAD: printf("P");break; | |
default:printf("?");assert(0);break; | |
} | |
printf("%d",cl); | |
} | |
printf("\n"); | |
printf("qual :"); | |
for(n=0;n<(b->core.l_qseq);n++) { | |
printf(" %d",qual[n]); | |
} | |
printf("\n\n"); | |
bam_destroy1(b); | |
b = bam_init1(); | |
} | |
bam_destroy1(b); | |
samclose(fp_in); | |
return 0; | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment