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, 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);
}