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sample.c

#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);
      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);
}

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