Imported Upstream version 0.5

[pysam.git] / samtools / sample.c.pysam.c

diff --git a/samtools/sample.c.pysam.c b/samtools/sample.c.pysam.c
new file mode 100644 (file)
index 0000000..dc8e627
--- /dev/null
+++ b/samtools/sample.c.pysam.c
@@ -0,0 +1,95 @@
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+       bam_sample_t *s;
+       s = calloc(1, sizeof(bam_sample_t));
+       s->rg2smid = kh_init(sm);
+       s->sm2id = kh_init(sm);
+       return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+       int i;
+       khint_t k;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       if (sm == 0) return;
+       for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+       free(sm->smpl);
+       for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+               if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+       kh_destroy(sm, sm->rg2smid);
+       kh_destroy(sm, sm->sm2id);
+       free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+       khint_t k_rg, k_sm;
+       int ret;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       k_rg = kh_get(sm, rg2smid, key);
+       if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+       k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+       k_sm = kh_get(sm, sm2id, val);
+       if (k_sm == kh_end(sm2id)) { // absent
+               if (sm->n == sm->m) {
+                       sm->m = sm->m? sm->m<<1 : 1;
+                       sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
+               }
+               sm->smpl[sm->n] = strdup(val);
+               k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+               kh_val(sm2id, k_sm) = sm->n++;
+       }
+       kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+       const char *p = txt, *q, *r;
+       kstring_t buf;
+       int n = 0;
+       khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+       memset(&buf, 0, sizeof(kstring_t));
+       while ((q = strstr(p, "@RG")) != 0) {
+               p = q + 3;
+               r = q = 0;
+               if ((q = strstr(p, "\tID:")) != 0) q += 4;
+               if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+               if (r && q) {
+                       char *u, *v;
+                       int oq, or;
+                       for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+                       for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+                       oq = *u; or = *v; *u = *v = '\0';
+                       buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+                       add_pair(sm, sm2id, buf.s, r);
+                       *u = oq; *v = or;
+               } else break;
+               p = q > r? q : r;
+               ++n;
+       }
+       if (n == 0) add_pair(sm, sm2id, fn, fn);
+//     add_pair(sm, sm2id, fn, fn);
+       free(buf.s);
+       return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+       khint_t k;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       if (rg) {
+               str->l = 0;
+               kputs(fn, str); kputc('/', str); kputs(rg, str);
+               k = kh_get(sm, rg2smid, str->s);
+       } else k = kh_get(sm, rg2smid, fn);
+       return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}