From 7e56a1610a2f932ba2ef66b0e89b1170b9c654e1 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 9 Feb 2010 14:46:09 +0000 Subject: [PATCH] Added the -d option to limit maximum depth for indels. --- bam_plcmd.c | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/bam_plcmd.c b/bam_plcmd.c index ccc5eb9..f8ae6b4 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -31,6 +31,7 @@ typedef struct { uint32_t format; int tid, len, last_pos; int mask; + int max_depth; // for indel calling, ignore reads with the depth too high. 0 for unlimited char *ref; glfFile fp_glf; // for glf output only } pu_data_t; @@ -124,10 +125,11 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, g3->offset = pos - d->last_pos; d->last_pos = pos; glf3_write1(d->fp_glf, g3); - if (pos < d->len) { + if (pos < d->len) { + int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth; if (proposed_indels) - r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); - else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); + else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0); } if (r) { // then write indel line int het = 3 * n, min; @@ -205,10 +207,11 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8; } else cns = bam_maqcns_call(n, pu, d->c); } - if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels - if (proposed_indels) // the first element gives the size of the array - r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); - else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels + int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth; + if (proposed_indels) // the first element gives the size of the array + r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); + else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0); } // when only variant sites are asked for, test if the site is a variant if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) { @@ -319,10 +322,11 @@ int bam_pileup(int argc, char *argv[]) int c, is_SAM = 0; char *fn_list = 0, *fn_fa = 0, *fn_pos = 0; pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t)); + d->max_depth = 0; d->tid = -1; d->mask = BAM_DEF_MASK; d->c = bam_maqcns_init(); d->ido = bam_maqindel_opt_init(); - while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2aR:")) >= 0) { + while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:")) >= 0) { switch (c) { case 'a': d->c->is_soap = 1; break; case 's': d->format |= BAM_PLF_SIMPLE; break; @@ -333,6 +337,7 @@ int bam_pileup(int argc, char *argv[]) case 'N': d->c->n_hap = atoi(optarg); break; case 'r': d->c->het_rate = atof(optarg); break; case 'M': d->c->cap_mapQ = atoi(optarg); break; + case 'd': d->max_depth = atoi(optarg); break; case 'c': d->format |= BAM_PLF_CNS; break; case 'i': d->format |= BAM_PLF_INDEL_ONLY; break; case 'v': d->format |= BAM_PLF_VAR_ONLY; break; @@ -362,6 +367,7 @@ int bam_pileup(int argc, char *argv[]) fprintf(stderr, " -i only show lines/consensus with indels\n"); fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask); fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ); + fprintf(stderr, " -d INT limit maximum depth for indels [unlimited]\n"); fprintf(stderr, " -t FILE list of reference sequences (force -S)\n"); fprintf(stderr, " -l FILE list of sites at which pileup is output\n"); fprintf(stderr, " -f FILE reference sequence in the FASTA format\n\n"); -- 2.39.2