#define BAM_PLF_INDEL_ONLY 0x04
#define BAM_PLF_GLF 0x08
#define BAM_PLF_VAR_ONLY 0x10
+#define BAM_PLF_2ND 0x20
+#define BAM_PLF_RANBASE 0x40
+#define BAM_PLF_1STBASE 0x80
+#define BAM_PLF_ALLBASE 0x100
typedef struct {
bam_header_t *h;
g3->offset = pos - d->last_pos;
d->last_pos = pos;
glf3_write1(d->fp_glf, g3);
- 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);
+ if (pos < d->len) {
+ 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);
+ }
if (r) { // then write indel line
int het = 3 * n, min;
min = het;
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 (d->format & BAM_PLF_CNS) { // call consensus
+ if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call
+ const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n);
+ int q = bam1_qual(p->b)[p->qpos];
+ int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+ uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos);
+ cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8;
+ } else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases
+ uint64_t rmsQ = 0;
+ uint32_t b = 0;
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pu + i;
+ int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+ b |= bam1_seqi(bam1_seq(p->b), p->qpos);
+ rmsQ += q * q;
+ }
+ rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499);
+ 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);
// 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
+ if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel
+ if (r) bam_maqindel_ret_destroy(r);
return 0;
+ }
}
}
// print the first 3 columns
if (c > 126) c = 126;
putchar(c);
}
+ if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities
+ const unsigned char *q;
+ putchar('\t');
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pu + i;
+ q = bam_aux_get(p->b, "E2");
+ putchar(q? q[p->qpos + 1] : 'N');
+ }
+ putchar('\t');
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pu + i;
+ q = bam_aux_get(p->b, "U2");
+ putchar(q? q[p->qpos + 1] : '!');
+ }
+ }
// print mapping quality if -s is flagged on the command line
if (d->format & BAM_PLF_SIMPLE) {
putchar('\t');
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);
+ printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
+ printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
bam_maqindel_ret_destroy(r);
}
return 0;
int bam_pileup(int argc, char *argv[])
{
- int c;
+ 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->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:")) >= 0) {
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2aR:")) >= 0) {
switch (c) {
+ case 'a': d->c->is_soap = 1; break;
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'l': fn_pos = strdup(optarg); 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 '2': d->format |= BAM_PLF_2ND; break;
case 'I': d->ido->q_indel = atoi(optarg); break;
case 'G': d->ido->r_indel = atof(optarg); break;
+ case 'S': is_SAM = 1; break;
+ case 'R':
+ if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE;
+ else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE;
+ else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE;
+ else fprintf(stderr, "[bam_pileup] unrecognized -R\n");
+ break;
default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
}
}
+ if (fn_list) is_SAM = 1;
if (optind == argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
+ fprintf(stderr, " -S the input is in SAM\n");
+ fprintf(stderr, " -a use the SOAPsnp model for SNP calling\n");
+ fprintf(stderr, " -2 output the 2nd best call and quality\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, " -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");
fprintf(stderr, " -c output the maq consensus sequence\n");
free(fn_list); free(fn_fa); free(d);
return 1;
}
+ if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS;
if (fn_fa) d->fai = fai_load(fn_fa);
if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
if (d->format & BAM_PLF_GLF) { // for glf output
}
if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
+ if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
+
{
samfile_t *fp;
- fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
+ fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
if (fp == 0 || fp->header == 0) {
fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
return 1;
projects / samtools.git / blobdiff