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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <getopt.h> |
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|
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#include "bam/bam.h" |
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#include "bam/sam.h" |
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|
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static bool is_fastq=true; //default is fastq |
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static bool sam_input=false; //default is BAM |
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|
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static char qseq[2048]; |
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|
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const char *short_options = "aq"; |
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|
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enum { |
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OPT_FASTA = 127, |
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OPT_FASTQ, |
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OPT_SAM |
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}; |
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|
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static struct option long_options[] = { |
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{"fasta", no_argument, 0, OPT_FASTA}, |
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{"fastq", no_argument, 0, OPT_FASTQ}, |
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{"sam", no_argument, 0, OPT_SAM}, |
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{0, 0, 0, 0} // terminator |
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}; |
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|
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int parse_options(int argc, char** argv) |
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{ |
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int option_index = 0; |
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int next_option; |
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do { |
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next_option = getopt_long(argc, argv, short_options, long_options, &option_index); |
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switch (next_option) { |
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case -1: |
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break; |
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case 'a': |
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case OPT_FASTA: |
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is_fastq = false; |
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break; |
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case 'q': |
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case OPT_FASTQ: |
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is_fastq = true; |
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break; |
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case 's': |
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case 't': |
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case OPT_SAM: //sam (text) input |
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sam_input = true; |
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break; |
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default: |
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return 1; |
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} |
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} while(next_option != -1); |
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|
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return 0; |
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} |
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|
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|
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void showfastq(const bam1_t *b, samfile_t* fp) { |
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//uint32_t *cigar = bam1_cigar(b); |
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//const bam1_core_t *c = &b->core; |
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char *name = bam1_qname(b); |
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char *qual = (char*)bam1_qual(b); |
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char *s = (char*)bam1_seq(b); |
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int i; |
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for(i=0;i<(b->core.l_qseq);i++) { |
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int8_t v = bam1_seqi(s,i); |
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qseq[i] = bam_nt16_rev_table[v]; |
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} |
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qseq[i] = 0; |
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|
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printf("@%s\n%s\n",name, qseq); |
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//print SAM text format of this BAM record: |
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//char * samtext=bam_format1(fp_in->header, b); |
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//printf("%s\n",samtext); |
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|
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//printf("s cigar: %s\n",cigar); |
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|
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//printf("qual : "); |
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for(i=0;i<(b->core.l_qseq);i++) { |
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//printf(" %d",qual[n]); |
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qseq[i]=qual[i]+33; |
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} |
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qseq[i]=0; |
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printf("+\n%s\n",qseq); |
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} |
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|
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void showfasta(const bam1_t *b, samfile_t* fp) { |
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char *name = bam1_qname(b); |
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char *s = (char*)bam1_seq(b); |
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int i; |
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for(i=0;i<(b->core.l_qseq);i++) { |
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int8_t v = bam1_seqi(s,i); |
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qseq[i] = bam_nt16_rev_table[v]; |
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} |
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qseq[i] = 0; |
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printf(">%s\n%s\n",name, qseq); |
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} |
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|
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|
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#define USAGE "Usage: bam2fastx [--fasta|-a|--fastq|-q] [--sam|-s|-t] <in.bam>|<in.sam> \n" |
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|
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int main(int argc, char *argv[]) |
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{ |
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samfile_t *fp; |
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char* fname=NULL; |
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|
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if (parse_options(argc, argv) || optind>=argc) { |
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fprintf(stderr, USAGE); |
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return -1; |
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} |
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fname=argv[optind++]; |
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|
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if (fname==NULL || fname[0]==0) { |
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fprintf(stderr, USAGE); |
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return 1; |
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} |
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if (sam_input) |
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fp = samopen(fname, "r", 0); |
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else |
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fp = samopen(fname, "rb", 0); |
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if (fp == 0) { |
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fprintf(stderr, "Error: bam2fastx failed to open BAM file %s\n", fname); |
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return 1; |
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} |
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|
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bam1_t *b = bam_init1(); |
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if (is_fastq) { |
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while (samread(fp, b) >= 0) showfastq(b, fp); |
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} |
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else { |
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while (samread(fp, b) >= 0) showfasta(b, fp); |
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} |
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|
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bam_destroy1(b); |
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|
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samclose(fp); |
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return 0; |
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} |
