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);
}