#define MPLP_GLF 0x10
#define MPLP_NO_COMP 0x20
+#define MPLP_NO_ORPHAN 0x40
+#define MPLP_REALN 0x80
+#define MPLP_NO_HALFTRIM 0x100
typedef struct {
int max_mq, min_mq, flag, min_baseQ;
typedef struct {
bamFile fp;
bam_iter_t iter;
- int min_mq;
+ int min_mq, flag;
+ char *ref;
} mplp_aux_t;
typedef struct {
static int mplp_func(void *data, bam1_t *b)
{
+ extern int bam_realn(bam1_t *b, const char *ref);
mplp_aux_t *ma = (mplp_aux_t*)data;
- int ret;
+ int ret, cond = 0;
do {
+ cond = 0;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
- } while (b->core.qual < ma->min_mq && ret >= 0);
+ if (ret < 0) break;
+ if (b->core.qual < ma->min_mq) cond = 1;
+ else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) cond = 1;
+ if (ma->ref && !cond && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
+ } while (cond);
return ret;
}
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->min_mq = conf->min_mq;
+ data[i]->flag = conf->flag;
data[i]->fp = bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
bam_smpl_add(sm, fn[i], h_tmp->text);
if (tid != ref_tid) {
free(ref);
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+ for (i = 0; i < n; ++i) data[i]->ref = ref;
ref_tid = tid;
}
if (conf->flag & MPLP_GLF) {
mplp.max_mq = 60;
mplp.theta = 1e-3;
mplp.min_baseQ = 13;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:u")) >= 0) {
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORH")) >= 0) {
switch (c) {
case 't': mplp.theta = atof(optarg); break;
case 'f':
case 'l': mplp.fn_pos = strdup(optarg); break;
case 'g': mplp.flag |= MPLP_GLF; break;
case 'u': mplp.flag |= MPLP_NO_COMP; break;
+ case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN | MPLP_NO_HALFTRIM; break;
+ case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
+ case 'H': mplp.flag |= MPLP_NO_HALFTRIM; break;
+ case 'R': mplp.flag |= MPLP_REALN; break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;
fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(stderr, " -t FLOAT scaled mutation rate [%lg]\n", mplp.theta);
- fprintf(stderr, " -g generate GLF output\n");
+ fprintf(stderr, " -g generate BCF output\n");
+ fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;