* samtools-0.1.5-12 (r415)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 1ff4a5aba25028f4fccdd0735a9dcae594b6e9a8..33907f1a68ce1d998ad19e8387d5c9acfdb58939 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -236,7 +236,7 @@ int bam_write1(bamFile fp, const bam1_t *b)
        return bam_write1_core(fp, &b->core, b->data_len, b->data);
 }
 
-char *bam_format1(const bam_header_t *header, const bam1_t *b)
+char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int is_hex)
 {
        uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
        int i;
@@ -244,7 +244,8 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        kstring_t str;
        str.l = str.m = 0; str.s = 0;
 
-       ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
+       if (is_hex) ksprintf(&str, "%s\t0x%x\t", bam1_qname(b), c->flag);
+       else ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
        if (c->tid < 0) kputs("*\t", &str);
        else ksprintf(&str, "%s\t", header->target_name[c->tid]);
        ksprintf(&str, "%d\t%d\t", c->pos + 1, c->qual);
@@ -282,6 +283,11 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        return str.s;
 }
 
+char *bam_format1(const bam_header_t *header, const bam1_t *b)
+{
+       return bam_format1_core(header, b, 0);
+}
+
 void bam_view1(const bam_header_t *header, const bam1_t *b)
 {
        char *s = bam_format1(header, b);