+#include <math.h>
#include <stdio.h>
#include <unistd.h>
#include <ctype.h>
#define BAM_PLF_CNS 0x02
#define BAM_PLF_INDEL_ONLY 0x04
#define BAM_PLF_GLF 0x08
+#define BAM_PLF_VAR_ONLY 0x10
typedef struct {
bam_header_t *h;
{
pu_data_t *d = (pu_data_t*)data;
bam_maqindel_ret_t *r = 0;
- int i, j, rb, rms_mapq = -1, max_mapq = 0, *proposed_indels = 0;
- uint32_t x;
+ int i, j, rb, rms_mapq = -1, *proposed_indels = 0;
+ uint64_t rms_aux;
+ uint32_t cns = 0;
+ // if GLF is required, suppress -c completely
if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data);
- if (d->hash) { // only output a list of sites
+ // if d->hash is initialized, only output the sites in the hash table
+ if (d->hash) {
khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
if (k == kh_end(d->hash)) return 0;
proposed_indels = kh_val(d->hash, k);
}
- if (d->fai && (int)tid != d->tid) { // then update d->ref
+ // update d->ref if necessary
+ if (d->fai && (int)tid != d->tid) {
free(d->ref);
d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
d->tid = tid;
}
rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
+ // when the indel-only mode is asked for, return if no reads mapped with indels
if (d->format & BAM_PLF_INDEL_ONLY) {
for (i = 0; i < n; ++i)
if (pu[i].indel != 0) break;
if (i == n) return 0;
}
+ // call the consensus and indel
+ if (d->format & BAM_PLF_CNS) // call consensus
+ cns = bam_maqcns_call(n, pu, d->c);
+ if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // 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);
+ }
+ // 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)) {
+ if (!(bam_nt16_table[rb] != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP
+ if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) // not an indel
+ return 0;
+ }
+ }
+ // print the first 3 columns
printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
- if (d->format & BAM_PLF_CNS) { // consensus
+ // print consensus information if required
+ if (d->format & BAM_PLF_CNS) {
int ref_q, rb4 = bam_nt16_table[rb];
- x = bam_maqcns_call(n, pu, d->c);
ref_q = 0;
- if (rb4 != 15 && x>>28 != 15 && x>>28 != rb4) { // a SNP
- ref_q = ((x>>24&0xf) == rb4)? x>>8&0xff : (x>>8&0xff) + (x&0xff);
+ if (rb4 != 15 && cns>>28 != 15 && cns>>28 != rb4) { // a SNP
+ ref_q = ((cns>>24&0xf) == rb4)? cns>>8&0xff : (cns>>8&0xff) + (cns&0xff);
if (ref_q > 255) ref_q = 255;
}
- printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff);
- rms_mapq = x>>16&0xff;
- }
- if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) {
- 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);
+ rms_mapq = cns>>16&0xff;
+ printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, ref_q, rms_mapq);
}
- // pileup strings
+ // print pileup sequences
printf("%d\t", n);
+ rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
for (i = 0; i < n; ++i) {
const bam_pileup1_t *p = pu + i;
- if (max_mapq < p->b->core.qual) max_mapq = p->b->core.qual;
+ int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+ rms_aux += tmp * tmp;
if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
if (!p->is_del) {
int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
} else putchar('*');
if (p->is_tail) putchar('$');
}
+ // finalize rms_mapq
+ rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
+ if (rms_mapq < 0) rms_mapq = rms_aux;
putchar('\t');
+ // print quality
for (i = 0; i < n; ++i) {
const bam_pileup1_t *p = pu + i;
int c = bam1_qual(p->b)[p->qpos] + 33;
if (c > 126) c = 126;
putchar(c);
}
+ // print mapping quality if -s is flagged on the command line
if (d->format & BAM_PLF_SIMPLE) {
putchar('\t');
for (i = 0; i < n; ++i) {
}
}
putchar('\n');
- if (r) { // then print indel line
+ // print the indel line if r has been calculated. This only happens if:
+ // a) -c or -i are flagged, AND b) the reference sequence is available
+ if (r) {
printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1);
if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]);
else printf("%s/%s\t", r->s[0], r->s[1]);
printf("%d\t%d\t", r->q_cns, r->q_ref);
- printf("%d\t%d\t", rms_mapq >= 0? rms_mapq : max_mapq, n);
+ printf("%d\t%d\t", rms_mapq, n);
printf("%s\t%s\t", r->s[0], r->s[1]);
//printf("%d\t%d\t", r->gl[0], r->gl[1]);
printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
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:")) >= 0) {
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) {
switch (c) {
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'T': d->c->theta = atof(optarg); break;
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 '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;
case 'm': d->mask = strtol(optarg, 0, 0); break;
case 'g': d->format |= BAM_PLF_GLF; break;
case 'I': d->ido->q_indel = atoi(optarg); break;
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
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, " -t FILE list of reference sequences (assume the input is in SAM)\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");
fprintf(stderr, " -c output the maq consensus sequence\n");
+ fprintf(stderr, " -v print variants only (for -c)\n");
fprintf(stderr, " -g output in the GLFv3 format (suppressing -c/-i/-s)\n");
fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
fprintf(stderr, " -N INT number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
projects / samtools.git / blobdiff