bam_flags.c

#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <unistd.h>
#include <stdarg.h>
#include <htslib/sam.h>

static void usage(void)
{
    fprintf(stderr, "\n");
    fprintf(stderr, "About: Convert between textual and numeric flag representation\n");
    fprintf(stderr, "Usage: samtools flags INT|STR[,...]\n");
    fprintf(stderr, "\n");
    fprintf(stderr, "Flags:\n");
    fprintf(stderr, "\t0x%x\tPAIRED        .. paired-end (or multiple-segment) sequencing technology\n", BAM_FPAIRED);
    fprintf(stderr, "\t0x%x\tPROPER_PAIR   .. each segment properly aligned according to the aligner\n", BAM_FPROPER_PAIR);
    fprintf(stderr, "\t0x%x\tUNMAP         .. segment unmapped\n", BAM_FUNMAP);
    fprintf(stderr, "\t0x%x\tMUNMAP        .. next segment in the template unmapped\n", BAM_FMUNMAP);
    fprintf(stderr, "\t0x%x\tREVERSE       .. SEQ is reverse complemented\n", BAM_FREVERSE);
    fprintf(stderr, "\t0x%x\tMREVERSE      .. SEQ of the next segment in the template is reversed\n", BAM_FMREVERSE);
    fprintf(stderr, "\t0x%x\tREAD1         .. the first segment in the template\n", BAM_FREAD1);
    fprintf(stderr, "\t0x%x\tREAD2         .. the last segment in the template\n", BAM_FREAD2);
    fprintf(stderr, "\t0x%x\tSECONDARY     .. secondary alignment\n", BAM_FSECONDARY);
    fprintf(stderr, "\t0x%x\tQCFAIL        .. not passing quality controls\n", BAM_FQCFAIL);
    fprintf(stderr, "\t0x%x\tDUP           .. PCR or optical duplicate\n", BAM_FDUP);
    fprintf(stderr, "\t0x%x\tSUPPLEMENTARY .. supplementary alignment\n", BAM_FSUPPLEMENTARY);
    fprintf(stderr, "\n");
}


int main_flags(int argc, char *argv[])
{
    if ( argc!=2 ) usage();
    else
    {
        int mask = bam_str2flag(argv[1]);
        if ( mask<0 ) { fprintf(stderr,"Error: Could not parse \"%s\"\n", argv[1]); usage(); return 1; }
        printf("0x%x\t%d\t%s\n", mask, mask, bam_flag2str(mask));
    }
	return 0;
}