#define MPLP_FMT_SP 0x200
#define MPLP_NO_INDEL 0x400
#define MPLP_EXT_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
typedef struct {
- int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
char *reg, *fn_pos, *pl_list;
skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
if (skip) continue;
}
+ if (ma->conf->flag & MPLP_ILLUMINA13) {
+ int i;
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i)
+ qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+ }
has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
skip = 0;
if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
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;
+ int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
max_depth = 8000 / sm->n;
fprintf(stderr, "<%s> Set max per-sample depth to %d\n", __func__, max_depth);
}
+ max_indel_depth = conf->max_indel_depth * sm->n;
bam_mplp_set_maxcnt(iter, max_depth);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
ref_tid = tid;
}
if (conf->flag & MPLP_GLF) {
- int _ref0, ref16;
+ int total_depth, _ref0, ref16;
bcf1_t *b = calloc(1, sizeof(bcf1_t));
+ for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = bam_nt16_table[_ref0];
bcf_write(bp, bh, b);
bcf_destroy(b);
// call indels
- if (!(conf->flag&MPLP_NO_INDEL) && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+ if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && 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) {
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
- mplp.max_depth = 250;
+ mplp.max_depth = 250; mplp.max_indel_depth = 250;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:Im:F:EG:")) >= 0) {
+ while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+ case '6': mplp.flag |= MPLP_ILLUMINA13; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'A': use_orphan = 1; break;
case 'F': mplp.min_frac = atof(optarg); break;
case 'm': mplp.min_support = atoi(optarg); break;
+ case 'L': mplp.max_indel_depth = atoi(optarg); break;
case 'G': {
FILE *fp_rg;
char buf[1024];
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
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, " -d INT max per-BAM depth [%d]\n", mplp.max_depth);
+ fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
+ fprintf(stderr, " -6 quality is in the Illumina-1.3+ encoding\n");
fprintf(stderr, " -A use anomalous read pairs in SNP/INDEL calling\n");
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
projects / samtools.git / blobdiff