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bam_plcmd.c
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bam_plcmd.c
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/* bam_plcmd.c -- mpileup subcommand.
Copyright (C) 2008-2015 Genome Research Ltd.
Portions copyright (C) 2009-2012 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <config.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>
#include <string.h>
#include <strings.h>
#include <limits.h>
#include <errno.h>
#include <sys/stat.h>
#include <getopt.h>
#include <htslib/sam.h>
#include <htslib/faidx.h>
#include <htslib/kstring.h>
#include <htslib/khash_str2int.h>
#include "sam_header.h"
#include "samtools.h"
#include "sam_opts.h"
static inline int printw(int c, FILE *fp)
{
char buf[16];
int l, x;
if (c == 0) return fputc('0', fp);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
buf[l] = 0;
for (x = 0; x < l/2; ++x) {
int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
}
fputs(buf, fp);
return 0;
}
static inline void pileup_seq(FILE *fp, const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
int j;
if (p->is_head) {
putc('^', fp);
putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
}
if (!p->is_del) {
int c = p->qpos < p->b->core.l_qseq
? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
: 'N';
if (ref) {
int rb = pos < ref_len? ref[pos] : 'N';
if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
} else {
if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
}
putc(c, fp);
} else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*', fp);
if (p->indel > 0) {
putc('+', fp); printw(p->indel, fp);
for (j = 1; j <= p->indel; ++j) {
int c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos + j)];
putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
}
} else if (p->indel < 0) {
printw(p->indel, fp);
for (j = 1; j <= -p->indel; ++j) {
int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
}
}
if (p->is_tail) putc('$', fp);
}
#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"
#define MPLP_BCF 1
#define MPLP_VCF (1<<1)
#define MPLP_NO_COMP (1<<2)
#define MPLP_NO_ORPHAN (1<<3)
#define MPLP_REALN (1<<4)
#define MPLP_NO_INDEL (1<<5)
#define MPLP_REDO_BAQ (1<<6)
#define MPLP_ILLUMINA13 (1<<7)
#define MPLP_IGNORE_RG (1<<8)
#define MPLP_PRINT_POS (1<<9)
#define MPLP_PRINT_MAPQ (1<<10)
#define MPLP_PER_SAMPLE (1<<11)
#define MPLP_SMART_OVERLAPS (1<<12)
#define MPLP_PRINT_QNAME (1<<13)
void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
typedef struct {
int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all;
int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
char *reg, *pl_list, *fai_fname, *output_fname;
faidx_t *fai;
void *bed, *rghash;
int argc;
char **argv;
sam_global_args ga;
} mplp_conf_t;
typedef struct {
char *ref[2];
int ref_id[2];
int ref_len[2];
} mplp_ref_t;
#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
typedef struct {
samFile *fp;
hts_itr_t *iter;
bam_hdr_t *h;
mplp_ref_t *ref;
const mplp_conf_t *conf;
} mplp_aux_t;
typedef struct {
int n;
int *n_plp, *m_plp;
bam_pileup1_t **plp;
} mplp_pileup_t;
static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, int *ref_len) {
mplp_ref_t *r = ma->ref;
//printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
if (!r || !ma->conf->fai) {
*ref = NULL;
return 0;
}
// Do we need to reference count this so multiple mplp_aux_t can
// track which references are in use?
// For now we just cache the last two. Sufficient?
if (tid == r->ref_id[0]) {
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
if (tid == r->ref_id[1]) {
// Last, swap over
int tmp;
tmp = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp;
tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp;
char *tc;
tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
// New, so migrate to old and load new
free(r->ref[1]);
r->ref[1] = r->ref[0];
r->ref_id[1] = r->ref_id[0];
r->ref_len[1] = r->ref_len[0];
r->ref_id[0] = tid;
r->ref[0] = faidx_fetch_seq(ma->conf->fai,
ma->h->target_name[r->ref_id[0]],
0,
INT_MAX,
&r->ref_len[0]);
if (!r->ref[0]) {
r->ref[0] = NULL;
r->ref_id[0] = -1;
r->ref_len[0] = 0;
*ref = NULL;
return 0;
}
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
static void
print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname,
int pos, int n, const char *ref, int ref_len)
{
int i;
fprintf(fp, "%s\t%d\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
fputs("\t0\t*\t*", fp);
if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", fp);
if (conf->flag & MPLP_PRINT_POS) fputs("\t*", fp);
if (conf->flag & MPLP_PRINT_QNAME) fputs("\t*", fp);
}
putc('\n', fp);
}
static int mplp_func(void *data, bam1_t *b)
{
char *ref;
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0, ref_len;
do {
int has_ref;
ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
if (ret < 0) break;
// The 'B' cigar operation is not part of the specification, considering as obsolete.
// bam_remove_B(b);
if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
skip = 1;
continue;
}
if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
if (ma->conf->bed && ma->conf->all == 0) { // test overlap
skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_endpos(b));
if (skip) continue;
}
if (ma->conf->rghash) { // exclude read groups
uint8_t *rg = bam_aux_get(b, "RG");
skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
if (skip) continue;
}
if (ma->conf->flag & MPLP_ILLUMINA13) {
int i;
uint8_t *qual = bam_get_qual(b);
for (i = 0; i < b->core.l_qseq; ++i)
qual[i] = qual[i] > 31? qual[i] - 31 : 0;
}
if (ma->conf->fai && b->core.tid >= 0) {
has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",
__func__, b->core.pos, ref_len, b->core.tid);
skip = 1;
continue;
}
} else {
has_ref = 0;
}
skip = 0;
if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
if (has_ref && ma->conf->capQ_thres > 10) {
int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
if (q < 0) skip = 1;
else if (b->core.qual > q) b->core.qual = q;
}
if (b->core.qual < ma->conf->min_mq) skip = 1;
else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
} while (skip);
return ret;
}
static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
{
int i, j;
memset(m->n_plp, 0, m->n * sizeof(int));
for (i = 0; i < n; ++i) {
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
uint8_t *q;
int id = -1;
q = ignore_rg? NULL : bam_aux_get(p->b, "RG");
if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
if (id < 0 || id >= m->n) {
assert(q); // otherwise a bug
fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
exit(EXIT_FAILURE);
}
if (m->n_plp[id] == m->m_plp[id]) {
m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
}
m->plp[id][m->n_plp[id]++] = *p;
}
}
}
/*
* Performs pileup
* @param conf configuration for this pileup
* @param n number of files specified in fn
* @param fn filenames
*/
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 = INT_MAX, tid0 = 0, ref_len, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
mplp_ref_t mp_ref = MPLP_REF_INIT;
bam_mplp_t iter;
bam_hdr_t *h = NULL; /* header of first file in input list */
char *ref;
void *rghash = NULL;
FILE *pileup_fp = NULL;
bcf_callaux_t *bca = NULL;
bcf_callret1_t *bcr = NULL;
bcf_call_t bc;
htsFile *bcf_fp = NULL;
bcf_hdr_t *bcf_hdr = NULL;
bam_sample_t *sm = NULL;
kstring_t buf;
mplp_pileup_t gplp;
memset(&gplp, 0, sizeof(mplp_pileup_t));
memset(&buf, 0, sizeof(kstring_t));
memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(mplp_aux_t*));
plp = calloc(n, sizeof(bam_pileup1_t*));
n_plp = calloc(n, sizeof(int));
sm = bam_smpl_init();
if (n == 0) {
fprintf(stderr,"[%s] no input file/data given\n", __func__);
exit(EXIT_FAILURE);
}
// read the header of each file in the list and initialize data
for (i = 0; i < n; ++i) {
bam_hdr_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
if ( !data[i]->fp )
{
fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
exit(EXIT_FAILURE);
}
if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
exit(EXIT_FAILURE);
}
if (conf->fai_fname && hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
fprintf(stderr, "[%s] failed to process %s: %s\n",
__func__, conf->fai_fname, strerror(errno));
exit(EXIT_FAILURE);
}
data[i]->conf = conf;
data[i]->ref = &mp_ref;
h_tmp = sam_hdr_read(data[i]->fp);
if ( !h_tmp ) {
fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
exit(EXIT_FAILURE);
}
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
// Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]);
if (idx == NULL) {
fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
exit(EXIT_FAILURE);
}
if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
exit(EXIT_FAILURE);
}
if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid;
hts_idx_destroy(idx);
}
else
data[i]->iter = NULL;
if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
else {
// FIXME: check consistency between h and h_tmp
bam_hdr_destroy(h_tmp);
// we store only the first file's header; it's (alleged to be)
// compatible with the i-th file's target_name lookup needs
data[i]->h = h;
}
}
// allocate data storage proportionate to number of samples being studied sm->n
gplp.n = sm->n;
gplp.n_plp = calloc(sm->n, sizeof(int));
gplp.m_plp = calloc(sm->n, sizeof(int));
gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*));
fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
// write the VCF header
if (conf->flag & MPLP_BCF)
{
const char *mode;
if ( conf->flag & MPLP_VCF )
mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz"; // uncompressed VCF or compressed VCF
else
mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb"; // uncompressed BCF or compressed BCF
bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
if (bcf_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
exit(EXIT_FAILURE);
}
// BCF header creation
bcf_hdr = bcf_hdr_init("w");
kstring_t str = {0,0,NULL};
ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
bcf_hdr_append(bcf_hdr, str.s);
str.l = 0;
ksprintf(&str, "##samtoolsCommand=samtools mpileup");
for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
kputc('\n', &str);
bcf_hdr_append(bcf_hdr, str.s);
if (conf->fai_fname)
{
str.l = 0;
ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
bcf_hdr_append(bcf_hdr, str.s);
}
// Translate BAM @SQ tags to BCF ##contig tags
// todo: use/write new BAM header manipulation routines, fill also UR, M5
for (i=0; i<h->n_targets; i++)
{
str.l = 0;
ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
bcf_hdr_append(bcf_hdr, str.s);
}
free(str.s);
bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
#if CDF_MWU_TESTS
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
#endif
bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
if ( conf->fmt_flag&B2B_FMT_DP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
if ( conf->fmt_flag&B2B_FMT_DV )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
if ( conf->fmt_flag&B2B_FMT_DPR )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_INFO_DPR )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_FMT_DP4 )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
if ( conf->fmt_flag&B2B_FMT_SP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
if ( conf->fmt_flag&B2B_FMT_AD )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
if ( conf->fmt_flag&B2B_FMT_ADF )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
if ( conf->fmt_flag&B2B_FMT_ADR )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
if ( conf->fmt_flag&B2B_INFO_AD )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
if ( conf->fmt_flag&B2B_INFO_ADF )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
if ( conf->fmt_flag&B2B_INFO_ADR )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
for (i=0; i<sm->n; i++)
bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
bcf_hdr_add_sample(bcf_hdr, NULL);
bcf_hdr_write(bcf_fp, bcf_hdr);
// End of BCF header creation
// Initialise the calling algorithm
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
bc.bcf_hdr = bcf_hdr;
bc.n = sm->n;
bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
if (conf->fmt_flag)
{
assert( sizeof(float)==sizeof(int32_t) );
bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
{
// first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
for (i=0; i<sm->n; i++)
{
bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
}
}
}
}
else {
pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
if (pileup_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
exit(EXIT_FAILURE);
}
}
// init pileup
iter = bam_mplp_init(n, mplp_func, (void**)data);
if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
max_depth = conf->max_depth;
if (max_depth * sm->n > 1<<20)
fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
if (max_depth * sm->n < 8000) {
max_depth = 8000 / sm->n;
fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
}
max_indel_depth = conf->max_indel_depth * sm->n;
bam_mplp_set_maxcnt(iter, max_depth);
bcf1_t *bcf_rec = bcf_init1();
int ret;
int last_tid = -1, last_pos = -1;
// begin pileup
while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
mplp_get_ref(data[0], tid, &ref, &ref_len);
//printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
if (conf->flag & MPLP_BCF) {
int total_depth, _ref0, ref16;
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = seq_nt16_table[_ref0];
bcf_callaux_clean(bca, &bc);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bc.tid = tid; bc.pos = pos;
bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
// call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
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)
{
bcf_callaux_clean(bca, &bc);
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, bca, -1, &bc) >= 0) {
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
}
}
} else {
if (conf->all) {
// Deal with missing portions of previous tids
while (tid > last_tid) {
if (last_tid >= 0 && !conf->reg) {
while (++last_pos < h->target_len[last_tid]) {
if (conf->bed && bed_overlap(conf->bed, h->target_name[last_tid], last_pos, last_pos + 1) == 0)
continue;
print_empty_pileup(pileup_fp, conf, h->target_name[last_tid], last_pos, n, ref, ref_len);
}
}
last_tid++;
last_pos = -1;
if (conf->all < 2)
break;
}
}
if (conf->all) {
// Deal with missing portion of current tid
while (++last_pos < pos) {
if (conf->reg && last_pos < beg0) continue; // out of range; skip
if (conf->bed && bed_overlap(conf->bed, h->target_name[tid], last_pos, last_pos + 1) == 0)
continue;
print_empty_pileup(pileup_fp, conf, h->target_name[tid], last_pos, n, ref, ref_len);
}
last_tid = tid;
last_pos = pos;
}
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
fprintf(pileup_fp, "%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
int j, cnt;
for (j = cnt = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ) ++cnt;
}
fprintf(pileup_fp, "\t%d\t", cnt);
if (n_plp[i] == 0) {
fputs("*\t*", pileup_fp);
if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", pileup_fp);
if (conf->flag & MPLP_PRINT_POS) fputs("\t*", pileup_fp);
if (conf->flag & MPLP_PRINT_QNAME) fputs("\t*", pileup_fp);
} else {
int n = 0;
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ)
n++, pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref);
}
if (!n) putc('*', pileup_fp);
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ) {
c = c + 33 < 126? c + 33 : 126;
putc(c, pileup_fp);
n++;
}
}
if (!n) putc('*', pileup_fp);
if (conf->flag & MPLP_PRINT_MAPQ) {
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = bam_get_qual(p->b)[p->qpos];
if ( c < conf->min_baseQ ) continue;
c = plp[i][j].b->core.qual + 33;
if (c > 126) c = 126;
putc(c, pileup_fp);
n++;
}
if (!n) putc('*', pileup_fp);
}
if (conf->flag & MPLP_PRINT_POS) {
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = bam_get_qual(p->b)[p->qpos];
if ( c < conf->min_baseQ ) continue;
if (n > 0) putc(',', pileup_fp);
fprintf(pileup_fp, "%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
n++;
}
if (!n) putc('*', pileup_fp);
}
if (conf->flag & MPLP_PRINT_QNAME) {
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = &plp[i][j];
int c = bam_get_qual(p->b)[p->qpos];
if ( c < conf->min_baseQ ) continue;
if (n > 0) putc(',', pileup_fp);
fputs(bam_get_qname(p->b), pileup_fp);
n++;
}
if (!n) putc('*', pileup_fp);
}
}
}
putc('\n', pileup_fp);
}
}
if (conf->all && !(conf->flag & MPLP_BCF)) {
// Handle terminating region
if (last_tid < 0 && conf->reg && conf->all > 1) {
last_tid = tid0;
last_pos = beg0-1;
mplp_get_ref(data[0], tid0, &ref, &ref_len);
}
while (last_tid >= 0 && last_tid < h->n_targets) {
while (++last_pos < h->target_len[last_tid]) {
if (last_pos >= end0) break;
if (conf->bed && bed_overlap(conf->bed, h->target_name[last_tid], last_pos, last_pos + 1) == 0)
continue;
print_empty_pileup(pileup_fp, conf, h->target_name[last_tid], last_pos, n, ref, ref_len);
}
last_tid++;
last_pos = -1;
if (conf->all < 2 || conf->reg)
break;
}
}
// clean up
free(bc.tmp.s);
bcf_destroy1(bcf_rec);
if (bcf_fp)
{
hts_close(bcf_fp);
bcf_hdr_destroy(bcf_hdr);
bcf_call_destroy(bca);
free(bc.PL);
free(bc.DP4);
free(bc.ADR);
free(bc.ADF);
free(bc.fmt_arr);
free(bcr);
}
if (pileup_fp && conf->output_fname) fclose(pileup_fp);
bam_smpl_destroy(sm); free(buf.s);
for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
bcf_call_del_rghash(rghash);
bam_mplp_destroy(iter);
bam_hdr_destroy(h);
for (i = 0; i < n; ++i) {
sam_close(data[i]->fp);
if (data[i]->iter) hts_itr_destroy(data[i]->iter);
free(data[i]);
}
free(data); free(plp); free(n_plp);
free(mp_ref.ref[0]);
free(mp_ref.ref[1]);
return ret;
}
static int is_url(const char *s)
{
static const char uri_scheme_chars[] =
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
return s[strspn(s, uri_scheme_chars)] == ':';
}
#define MAX_PATH_LEN 1024
int read_file_list(const char *file_list,int *n,char **argv[])
{
char buf[MAX_PATH_LEN];
int len, nfiles = 0;
char **files = NULL;
struct stat sb;
*n = 0;
*argv = NULL;
FILE *fh = fopen(file_list,"r");
if ( !fh )
{
fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
return 1;
}
files = calloc(nfiles,sizeof(char*));
nfiles = 0;
while ( fgets(buf,MAX_PATH_LEN,fh) )
{
// allow empty lines and trailing spaces
len = strlen(buf);
while ( len>0 && isspace(buf[len-1]) ) len--;
if ( !len ) continue;
// check sanity of the file list
buf[len] = 0;
if (! (is_url(buf) || stat(buf, &sb) == 0))
{
// no such file, check if it is safe to print its name
int i, safe_to_print = 1;
for (i=0; i<len; i++)
if (!isprint(buf[i])) { safe_to_print = 0; break; }
if ( safe_to_print )
fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
else
fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
return 1;
}
nfiles++;
files = realloc(files,nfiles*sizeof(char*));
files[nfiles-1] = strdup(buf);
}
fclose(fh);
if ( !nfiles )
{
fprintf(stderr,"No files read from %s\n", file_list);
return 1;
}
*argv = files;
*n = nfiles;
return 0;
}
#undef MAX_PATH_LEN
int parse_format_flag(const char *str)
{
int i, flag = 0, n_tags;
char **tags = hts_readlist(str, 0, &n_tags);
for(i=0; i<n_tags; i++)
{
if ( !strcasecmp(tags[i],"DP") ) flag |= B2B_FMT_DP;
else if ( !strcasecmp(tags[i],"DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
else if ( !strcasecmp(tags[i],"SP") ) flag |= B2B_FMT_SP;
else if ( !strcasecmp(tags[i],"DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
else if ( !strcasecmp(tags[i],"DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
else if ( !strcasecmp(tags[i],"AD") ) flag |= B2B_FMT_AD;
else if ( !strcasecmp(tags[i],"ADF") ) flag |= B2B_FMT_ADF;
else if ( !strcasecmp(tags[i],"ADR") ) flag |= B2B_FMT_ADR;
else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
else
{
fprintf(stderr,"Could not parse tag \"%s\" in \"%s\"\n", tags[i], str);
exit(EXIT_FAILURE);
}
free(tags[i]);
}
if (n_tags) free(tags);
return flag;
}
static void print_usage(FILE *fp, const mplp_conf_t *mplp)
{
char *tmp_require = bam_flag2str(mplp->rflag_require);
char *tmp_filter = bam_flag2str(mplp->rflag_filter);
// Display usage information, formatted for the standard 80 columns.
// (The unusual string formatting here aids the readability of this
// source code in 80 columns, to the extent that's possible.)
fprintf(fp,
"\n"
"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
"\n"
"Input options:\n"
" -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding\n"
" -A, --count-orphans do not discard anomalous read pairs\n"
" -b, --bam-list FILE list of input BAM filenames, one per line\n"
" -B, --no-BAQ disable BAQ (per-Base Alignment Quality)\n"
" -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]\n"
" -d, --max-depth INT max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
fprintf(fp,
" -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs\n"
" -f, --fasta-ref FILE faidx indexed reference sequence file\n"
" -G, --exclude-RG FILE exclude read groups listed in FILE\n"
" -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)\n"
" -q, --min-MQ INT skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
fprintf(fp,
" -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
fprintf(fp,
" -r, --region REG region in which pileup is generated\n"
" -R, --ignore-RG ignore RG tags (one BAM = one sample)\n"
" --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [%s]\n", tmp_require);
fprintf(fp,
" --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set\n"
" [%s]\n", tmp_filter);
fprintf(fp,
" -x, --ignore-overlaps disable read-pair overlap detection\n"
"\n"
"Output options:\n"
" -o, --output FILE write output to FILE [standard output]\n"
" -g, --BCF generate genotype likelihoods in BCF format\n"
" -v, --VCF generate genotype likelihoods in VCF format\n"
"\n"
"Output options for mpileup format (without -g/-v):\n"
" -O, --output-BP output base positions on reads\n"
" -s, --output-MQ output mapping quality\n"
" --output-QNAME output read names\n"
" -a output all positions (including zero depth)\n"
" -a -a (or -aa) output absolutely all positions, including unused ref. sequences\n"
"\n"
"Output options for genotype likelihoods (when -g/-v is used):\n"
" -t, --output-tags LIST optional tags to output:\n"
" DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR []\n"
" -u, --uncompressed generate uncompressed VCF/BCF output\n"
"\n"
"SNP/INDEL genotype likelihoods options (effective with -g/-v):\n"
" -e, --ext-prob INT Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
fprintf(fp,
" -F, --gap-frac FLOAT minimum fraction of gapped reads [%g]\n", mplp->min_frac);
fprintf(fp,
" -h, --tandem-qual INT coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
fprintf(fp,
" -I, --skip-indels do not perform indel calling\n"
" -L, --max-idepth INT maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth);
fprintf(fp,
" -m, --min-ireads INT minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
fprintf(fp,
" -o, --open-prob INT Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
fprintf(fp,
" -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity\n"
" -P, --platforms STR comma separated list of platforms for indels [all]\n");
sam_global_opt_help(fp, "-.--.-");
fprintf(fp,
"\n"
"Notes: Assuming diploid individuals.\n");
free(tmp_require);
free(tmp_filter);
}
int bam_mpileup(int argc, char *argv[])
{
int c;
const char *file_list = NULL;
char **fn = NULL;
int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
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 | MPLP_SMART_OVERLAPS;
mplp.argc = argc; mplp.argv = argv;
mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
mplp.output_fname = NULL;
mplp.all = 0;
sam_global_args_init(&mplp.ga);
static const struct option lopts[] =
{
SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
{"rf", required_argument, NULL, 1}, // require flag
{"ff", required_argument, NULL, 2}, // filter flag
{"incl-flags", required_argument, NULL, 1},
{"excl-flags", required_argument, NULL, 2},
{"output", required_argument, NULL, 3},
{"open-prob", required_argument, NULL, 4},
{"output-QNAME", no_argument, NULL, 5},
{"output-qname", no_argument, NULL, 5},
{"illumina1.3+", no_argument, NULL, '6'},
{"count-orphans", no_argument, NULL, 'A'},
{"bam-list", required_argument, NULL, 'b'},
{"no-BAQ", no_argument, NULL, 'B'},
{"no-baq", no_argument, NULL, 'B'},
{"adjust-MQ", required_argument, NULL, 'C'},
{"adjust-mq", required_argument, NULL, 'C'},
{"max-depth", required_argument, NULL, 'd'},
{"redo-BAQ", no_argument, NULL, 'E'},
{"redo-baq", no_argument, NULL, 'E'},
{"fasta-ref", required_argument, NULL, 'f'},
{"exclude-RG", required_argument, NULL, 'G'},
{"exclude-rg", required_argument, NULL, 'G'},
{"positions", required_argument, NULL, 'l'},
{"region", required_argument, NULL, 'r'},
{"ignore-RG", no_argument, NULL, 'R'},
{"ignore-rg", no_argument, NULL, 'R'},