* change the order of PL/GL according to the latest VCF spec

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index fb70d81ae8c1c50d765176860c55719388f5b260..ae7ec0f0256f2bff77ad12d31f8c05ece2f518a0 100644 (file)
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -29,6 +29,16 @@ void bcf_str2id_destroy(void *_hash)
        if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
 }
 
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+       khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+       khint_t k;
+       if (hash == 0) return;
+       for (k = 0; k < kh_end(hash); ++k)
+               if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+       kh_destroy(str2id, hash);
+}
+
 int bcf_str2id(void *_hash, const char *str)
 {
        khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
@@ -53,8 +63,9 @@ int bcf_str2id_add(void *_hash, const char *str)
 int bcf_shrink_alt(bcf1_t *b, int n)
 {
        char *p;
-       int i, j, k, *z, n_smpl = b->n_smpl;
+       int i, j, k, n_smpl = b->n_smpl;
        if (b->n_alleles <= n) return -1;
+       // update ALT
        if (n > 1) {
                for (p = b->alt, k = 1; *p; ++p)
                        if (*p == ',' && ++k == n) break;
@@ -63,10 +74,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
        ++p;
        memmove(p, b->flt, b->str + b->l_str - b->flt);
        b->l_str -= b->flt - p;
-       z = alloca(sizeof(int) / 2 * n * (n+1));
-       for (i = k = 0; i < n; ++i)
-               for (j = 0; j < n - i; ++j)
-                       z[k++] = i * b->n_alleles + j;
+       // update PL
        for (i = 0; i < b->n_gi; ++i) {
                bcf_ginfo_t *g = b->gi + i;
                if (g->fmt == bcf_str2int("PL", 2)) {
@@ -75,7 +83,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
                        g->len = n * (n + 1) / 2;
                        for (l = k = 0; l < n_smpl; ++l) {
                                uint8_t *dl = d + l * x;
-                               for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
+                               for (j = 0; j < g->len; ++j) d[k++] = dl[j];
                        }
                } // FIXME: to add GL
        }
@@ -147,7 +155,8 @@ int bcf_anno_max(bcf1_t *b)
 {
        int k, max_gq, max_sp, n_het;
        kstring_t str;
-       uint8_t *gt, *gq, *sp;
+       uint8_t *gt, *gq;
+       int32_t *sp;
        max_gq = max_sp = n_het = 0;
        gt = locate_field(b, "GT", 2);
        if (gt == 0) return -1;