X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=fd75cec8c8841a1f174731dc2eeef603571b86d2;hp=bba62cbcdcabe52cbdba71ab71a6b2e5681aa032;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=c34624801b980425af68c3c431423c72b18c14fe diff --git a/bam_plcmd.c b/bam_plcmd.c index bba62cb..fd75cec 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -534,9 +534,10 @@ int bam_pileup(int argc, char *argv[]) #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; @@ -575,6 +576,12 @@ static int mplp_func(void *data, bam1_t *b) 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); @@ -617,7 +624,7 @@ 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; + 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; @@ -722,6 +729,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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 @@ -737,8 +745,9 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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]; @@ -750,7 +759,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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) { @@ -866,11 +875,11 @@ int bam_mpileup(int argc, char *argv[]) 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); @@ -889,6 +898,7 @@ int bam_mpileup(int argc, char *argv[]) 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; @@ -900,6 +910,7 @@ int bam_mpileup(int argc, char *argv[]) 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]; @@ -924,7 +935,8 @@ int bam_mpileup(int argc, char *argv[]) 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); @@ -932,6 +944,7 @@ int bam_mpileup(int argc, char *argv[]) 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");