https://github.com/samtools/samtools
Tip revision: 0746c10643c92a4e8c7dc9663b2cc0c63249e683 authored by Heng Li on 02 September 2009, 12:56:33 UTC
Release samtools-0.1.6
Release samtools-0.1.6
Tip revision: 0746c10
bam_plcmd.c
#include <math.h>
#include <stdio.h>
#include <unistd.h>
#include <ctype.h>
#include "sam.h"
#include "faidx.h"
#include "bam_maqcns.h"
#include "khash.h"
#include "glf.h"
#include "kstring.h"
typedef int *indel_list_t;
KHASH_MAP_INIT_INT64(64, indel_list_t)
#define BAM_PLF_SIMPLE 0x01
#define BAM_PLF_CNS 0x02
#define BAM_PLF_INDEL_ONLY 0x04
#define BAM_PLF_GLF 0x08
#define BAM_PLF_VAR_ONLY 0x10
#define BAM_PLF_2ND 0x20
typedef struct {
bam_header_t *h;
bam_maqcns_t *c;
bam_maqindel_opt_t *ido;
faidx_t *fai;
khash_t(64) *hash;
uint32_t format;
int tid, len, last_pos;
int mask;
char *ref;
glfFile fp_glf; // for glf output only
} pu_data_t;
char **__bam_get_lines(const char *fn, int *_n);
void bam_init_header_hash(bam_header_t *header);
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
{
char **list;
int i, j, n, *fields, max_fields;
khash_t(64) *hash;
bam_init_header_hash(h);
list = __bam_get_lines(fn, &n);
hash = kh_init(64);
max_fields = 0; fields = 0;
for (i = 0; i < n; ++i) {
char *str = list[i];
int chr, n_fields, ret;
khint_t k;
uint64_t x;
n_fields = ksplit_core(str, 0, &max_fields, &fields);
if (n_fields < 2) continue;
chr = bam_get_tid(h, str + fields[0]);
if (chr < 0) {
fprintf(stderr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]);
continue;
}
x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1);
k = kh_put(64, hash, x, &ret);
if (ret == 0) {
fprintf(stderr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]);
continue;
}
kh_val(hash, k) = 0;
if (n_fields > 2) {
// count
for (j = 2; j < n_fields; ++j) {
char *s = str + fields[j];
if ((*s != '+' && *s != '-') || !isdigit(s[1])) break;
}
if (j > 2) { // update kh_val()
int *q, y, z;
q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int));
q[0] = j - 2; z = j; y = 1;
for (j = 2; j < z; ++j)
q[y++] = atoi(str + fields[j]);
}
}
free(str);
}
free(list); free(fields);
return hash;
}
// an analogy to pileup_func() below
static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
{
pu_data_t *d = (pu_data_t*)data;
bam_maqindel_ret_t *r = 0;
int rb, *proposed_indels = 0;
glf1_t *g;
glf3_t *g3;
if (d->fai == 0) {
fprintf(stderr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n");
exit(1);
}
if (d->hash) { // only output a list of sites
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);
}
g3 = glf3_init1();
if (d->fai && (int)tid != d->tid) {
if (d->ref) { // then write the end mark
g3->rtype = GLF3_RTYPE_END;
glf3_write1(d->fp_glf, g3);
}
glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference
free(d->ref);
d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
d->tid = tid;
d->last_pos = 0;
}
rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
memcpy(g3, g, sizeof(glf1_t));
g3->rtype = GLF3_RTYPE_SUB;
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 (r) { // then write indel line
int het = 3 * n, min;
min = het;
if (min > r->gl[0]) min = r->gl[0];
if (min > r->gl[1]) min = r->gl[1];
g3->ref_base = 0;
g3->rtype = GLF3_RTYPE_INDEL;
memset(g3->lk, 0, 10);
g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
g3->lk[2] = het - min < 255? het - min : 255;
g3->offset = 0;
g3->indel_len[0] = r->indel1;
g3->indel_len[1] = r->indel2;
g3->min_lk = min < 255? min : 255;
g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
g3->indel_seq[0] = strdup(r->s[0]+1);
g3->indel_seq[1] = strdup(r->s[1]+1);
glf3_write1(d->fp_glf, g3);
bam_maqindel_ret_destroy(r);
}
free(g);
glf3_destroy1(g3);
return 0;
}
static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
{
pu_data_t *d = (pu_data_t*)data;
bam_maqindel_ret_t *r = 0;
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 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);
}
// 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
if (r) bam_maqindel_ret_destroy(r);
return 0;
}
}
}
// print the first 3 columns
printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
// print consensus information if required
if (d->format & BAM_PLF_CNS) {
int ref_q, rb4 = bam_nt16_table[rb];
ref_q = 0;
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;
}
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);
}
// 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;
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)];
if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
else c = bam1_strand(p->b)? tolower(c) : toupper(c);
putchar(c);
if (p->indel > 0) {
printf("+%d", p->indel);
for (j = 1; j <= p->indel; ++j) {
c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
}
} else if (p->indel < 0) {
printf("%d", p->indel);
for (j = 1; j <= -p->indel; ++j) {
c = (d->ref && (int)pos+j < d->len)? d->ref[pos+j] : 'N';
putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
}
}
} 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);
}
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');
for (i = 0; i < n; ++i) {
int c = pu[i].b->core.qual + 33;
if (c > 126) c = 126;
putchar(c);
}
}
putchar('\n');
// 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, 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\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, 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:S2")) >= 0) {
switch (c) {
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'l': fn_pos = strdup(optarg); break;
case 'f': fn_fa = 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 '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;
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, " -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 (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");
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);
fprintf(stderr, " -r FLOAT prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
fprintf(stderr, " -G FLOAT prior of an indel between two haplotypes (for -c/-g) [%f]\n", d->ido->r_indel);
fprintf(stderr, " -I INT phred prob. of an indel in sequencing/prep. (for -c/-g) [%d]\n", d->ido->q_indel);
fprintf(stderr, "\n");
free(fn_list); free(fn_fa); free(d);
return 1;
}
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
glf3_header_t *h;
h = glf3_header_init();
d->fp_glf = bgzf_fdopen(fileno(stdout), "w");
glf3_header_write(d->fp_glf, h);
glf3_header_destroy(h);
}
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 = 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;
}
d->h = fp->header;
if (fn_pos) d->hash = load_pos(fn_pos, d->h);
sampileup(fp, d->mask, pileup_func, d);
samclose(fp); // d->h will be destroyed here
}
// free
if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf);
if (fn_pos) { // free the hash table
khint_t k;
for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
kh_destroy(64, d->hash);
}
free(fn_pos); free(fn_list); free(fn_fa);
if (d->fai) fai_destroy(d->fai);
bam_maqcns_destroy(d->c);
free(d->ido); free(d->ref); free(d);
return 0;
}