added the haploid mode

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index e6a132b8d1a11714f1734cf754fe40bd48afa23f..fc1c542c2d6a5142274ef157a10af31a99c88269 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;
@@ -178,3 +187,44 @@ int bcf_anno_max(bcf1_t *b)
        free(str.s);
        return 0;
 }
+
+bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
+{
+       int i, ret, j;
+       khint_t k;
+       bcf_hdr_t *h;
+       khash_t(str2id) *hash;
+       kstring_t s;
+       s.l = s.m = 0; s.s = 0;
+       hash = kh_init(str2id);
+       for (i = 0; i < n; ++i)
+               k = kh_put(str2id, hash, samples[i], &ret);
+       for (i = j = 0; i < h0->n_smpl; ++i) {
+               if (kh_get(str2id, hash, h0->sns[i]) != kh_end(hash)) {
+                       list[j++] = i;
+                       kputs(h0->sns[i], &s); kputc('\0', &s);
+               }
+       }
+       if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+       kh_destroy(str2id, hash);
+       h = calloc(1, sizeof(bcf_hdr_t));
+       *h = *h0;
+       h->ns = 0; h->sns = 0;
+       h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
+       h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
+       h->l_smpl = s.l; h->sname = s.s;
+       bcf_hdr_sync(h);
+       return h;
+}
+
+int bcf_subsam(int n_smpl, int *list, bcf1_t *b) // list MUST BE sorted
+{
+       int i, j;
+       for (j = 0; j < b->n_gi; ++j) {
+               bcf_ginfo_t *gi = b->gi + j;
+               for (i = 0; i < n_smpl; ++i)
+                       if (i != list[i]) memcpy((uint8_t*)gi->data + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+       }
+       b->n_smpl = n_smpl;
+       return 0;
+}