text: #include <stdlib.h>
  #include <string.h>
  #include "sample.h"
  #include "htslib/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(char*) * 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, first_sm;
  	int n = 0;
  	khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
  	if (txt == 0) {
  		add_pair(sm, sm2id, fn, fn);
  		return 0;
  	}
  	memset(&buf, 0, sizeof(kstring_t));
      memset(&first_sm, 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);
              if ( !first_sm.s )
                  kputs(r,&first_sm); 
  			*u = oq; *v = or;
  		} else break;
  		p = q > r? q : r;
  		++n;
  	}
  	if (n == 0) add_pair(sm, sm2id, fn, fn);
      // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
      //  use the tag instead.
      else if ( n==1 && first_sm.s )
          add_pair(sm,sm2id,fn,first_sm.s);
      if ( first_sm.s )
          free(first_sm.s);
  
  //	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);
  }
  