print QUAL as floating numbers

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index c3313881ef90fc2930c72d218c090b35e5cf9466..8801cea00a23feaea70e7cc40a736f580e9f17c1 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -146,13 +146,12 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 
 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 {
-       uint32_t x;
        int i, l = 0;
        if (b == 0) return -1;
        bgzf_write(bp->fp, &b->tid, 4);
        bgzf_write(bp->fp, &b->pos, 4);
-       x = b->qual<<24 | b->l_str;
-       bgzf_write(bp->fp, &x, 4);
+       bgzf_write(bp->fp, &b->qual, 4);
+       bgzf_write(bp->fp, &b->l_str, 4);
        bgzf_write(bp->fp, b->str, b->l_str);
        l = 12 + b->l_str;
        for (i = 0; i < b->n_gi; ++i) {
@@ -165,12 +164,11 @@ int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 {
        int i, l = 0;
-       uint32_t x;
        if (b == 0) return -1;
        if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
        bgzf_read(bp->fp, &b->pos, 4);
-       bgzf_read(bp->fp, &x, 4);
-       b->qual = x >> 24; b->l_str = x << 8 >> 8;
+       bgzf_read(bp->fp, &b->qual, 4);
+       bgzf_read(bp->fp, &b->l_str, 4);
        if (b->l_str > b->m_str) {
                b->m_str = b->l_str;
                kroundup32(b->m_str);
@@ -215,7 +213,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
        fmt_str(b->str, s); kputc('\t', s);
        fmt_str(b->ref, s); kputc('\t', s);
        fmt_str(b->alt, s); kputc('\t', s);
-       kputw(b->qual, s); kputc('\t', s);
+       ksprintf(s, "%.3g", b->qual); /*kputw(b->qual, s);*/ kputc('\t', s);
        fmt_str(b->flt, s); kputc('\t', s);
        fmt_str(b->info, s);
        if (b->fmt[0]) {