typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
- char *reg, *fn_pos;
+ char *reg, *fn_pos, *pl_list;
faidx_t *fai;
kh_64_t *hash;
} mplp_conf_t;
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
+ extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
+ extern void bcf_call_del_rghash(void *rghash);
mplp_aux_t **data;
int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
const bam_pileup1_t **plp;
bam_header_t *h = 0;
char *ref;
khash_t(64) *hash = 0;
+ void *rghash = 0;
bcf_callaux_t *bca = 0;
bcf_callret1_t *bcr = 0;
data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
bam_smpl_add(sm, fn[i], h_tmp->text);
+ rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
int beg, end;
bam_index_t *idx;
bcf_hdr_write(bp, bh);
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+ bca->rghash = rghash;
}
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bcf_call_combine(gplp.n, bcr, ref16, &bc);
- bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP), 0, 0);
bcf_write(bp, bh, b);
bcf_destroy(b);
+ // call indels
+ if (bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
+ if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
+ b = calloc(1, sizeof(bcf1_t));
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP), bca, ref);
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ }
+ }
} else {
printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
bam_smpl_destroy(sm); free(buf.s);
for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+ bcf_call_del_rghash(rghash);
if (hash) { // free the hash table
khint_t k;
for (k = kh_begin(hash); k < kh_end(hash); ++k)
mplp.capQ_thres = 0;
mplp.max_depth = 250;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:")) >= 0) {
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); break;
+ case 'P': mplp.pl_list = strdup(optarg); break;
case 'g': mplp.flag |= MPLP_GLF; break;
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; 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, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
+ fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
}
else
mpileup(&mplp, argc - optind, argv + optind);
- free(mplp.reg);
+ free(mplp.reg); free(mplp.pl_list);
if (mplp.fai) fai_destroy(mplp.fai);
return 0;
}