* samtools-0.1.8-10 (r658)

 * fixed a bug in bam2bcf when the reference is N

diff --git a/bamtk.c b/bamtk.c
index e3b71fea8c64e6675ed9797eaf9ba2375940bacb..863ba33e0e0b345db99bb33387289dab856c72a2 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-9 (r649)"
+#define PACKAGE_VERSION "0.1.8-10 (r658)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/bcf.c b/bcf.c
index 7286acaf9912744d15ec516ad695bc23801e35b1..f8b55c2cf02161828e4faa35665ca12d986978cc 100644 (file)
--- a/bcf.c
+++ b/bcf.c
@@ -52,6 +52,19 @@ int bcf_hdr_write(bcf_t *b)
        return 16 + h->l_nm + h->l_smpl + h->l_txt;
 }
 
+int bcf_hdr_cpy(bcf_hdr_t *h, const bcf_hdr_t *h0)
+{
+       *h = *h0;
+       h->name = malloc(h->l_nm);
+       h->sname = malloc(h->l_smpl);
+       h->txt = malloc(h->l_txt);
+       memcpy(h->name, h0->name, h->l_nm);
+       memcpy(h->sname, h0->sname, h->l_smpl);
+       memcpy(h->txt, h0->txt, h->l_txt);
+       bcf_hdr_sync(h);
+       return 0;
+}
+
 int bcf_hdr_read(bcf_t *b)
 {
        uint8_t magic[4];
@@ -102,7 +115,7 @@ int bcf_hdr_sync(bcf_hdr_t *b)
 int bcf_sync(int n_smpl, bcf1_t *b)
 {
        char *p, *tmp[5], *s;
-       int i, n, c;
+       int i, n;
        // set ref, alt, flt, info, fmt
        b->ref = b->alt = b->flt = b->info = b->fmt = 0;
        for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
@@ -112,10 +125,7 @@ int bcf_sync(int n_smpl, bcf1_t *b)
        // set n_alleles
        for (p = b->alt, n = 1; *p; ++p)
                if (*p == ',') ++n;
-       b->n_alleles = n;
-       c = toupper(*b->ref);
-       if (b->alt - b->ref == 2 && (c == 'A' || c == 'C' || c == 'G' || c == 'T'))
-               ++b->n_alleles;
+       b->n_alleles = n + 1;
        // set n_gi and gi[i].fmt
        for (p = b->fmt, n = 1; *p; ++p)
                if (*p == ':') ++n;
@@ -223,8 +233,11 @@ char *bcf_fmt(bcf_t *bp, bcf1_t *b)
        fmt_str(b->alt, &s); kputc('\t', &s);
        kputw(b->qual, &s); kputc('\t', &s);
        fmt_str(b->flt, &s); kputc('\t', &s);
-       fmt_str(b->info, &s); kputc('\t', &s);
-       fmt_str(b->fmt, &s);
+       fmt_str(b->info, &s);
+       if (b->fmt[0]) {
+               kputc('\t', &s);
+               fmt_str(b->fmt, &s);
+       }
        x = b->n_alleles * (b->n_alleles + 1) / 2;
        for (j = 0; j < bp->h.n_smpl; ++j) {
                kputc('\t', &s);