| c1100b9b |
#include <math.h>
#include <stdio.h>
#include <unistd.h>
#include <ctype.h>
#include <string.h>
#include <errno.h>
#include <sys/stat.h>
#include <getopt.h>
#include "sam.h"
#include "faidx.h"
#include "kstring.h"
#include "sam_header.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(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
int j;
/* if (p->is_head) {
putchar('^');
putchar(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 (ref) {
int rb = pos < ref_len? ref[pos] : 'N';
if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
else c = bam1_strand(p->b)? tolower(c) : toupper(c);
} else {
if (c == '=') c = bam1_strand(p->b)? ',' : '.';
else c = bam1_strand(p->b)? tolower(c) : toupper(c);
}
putchar(c);
} else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
if (p->indel > 0) {
putchar('+'); printw(p->indel, stdout);
for (j = 1; j <= p->indel; ++j) {
int 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) {
printw(p->indel, stdout);
for (j = 1; j <= -p->indel; ++j) {
int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
}
}
putchar('|');
// if (p->is_tail) putchar('$');
}
#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"
#define MPLP_GLF 0x10
#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN 0x80
#define MPLP_NO_INDEL 0x400
#define MPLP_REDO_BAQ 0x800
#define MPLP_ILLUMINA13 0x1000
#define MPLP_IGNORE_RG 0x2000
#define MPLP_PRINT_POS 0x4000
#define MPLP_PRINT_MAPQ 0x8000
#define MPLP_PER_SAMPLE 0x10000
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 max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
char *reg, *pl_list, *fai_fname;
faidx_t *fai;
void *bed, *rghash;
} mplp_conf_t;
typedef struct {
bamFile fp;
bam_iter_t iter;
bam_header_t *h;
int ref_id;
char *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_func(void *data, bam1_t *b)
{
extern int bam_realn(bam1_t *b, const char *ref);
extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
do {
int has_ref;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
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) { // test overlap
skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
if (skip) continue;
}
if (ma->conf->rghash) { // exclude read groups
uint8_t *rg = bam_aux_get(b, "RG");
skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
if (skip) continue;
}
if (ma->conf->flag & MPLP_ILLUMINA13) {
int i;
uint8_t *qual = bam1_qual(b);
for (i = 0; i < b->core.l_qseq; ++i)
qual[i] = qual[i] > 31? qual[i] - 31 : 0;
}
has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
skip = 0;
if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
if (has_ref && ma->conf->capQ_thres > 10) {
int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
if (q < 0) skip = 1;
else if (b->core.qual > q) b->core.qual = q;
}
else if (b->core.qual < ma->conf->min_mq) skip = 1;
else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) 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? 0 : 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(1);
}
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;
}
}
}
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, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
char *ref;
void *rghash = 0;
bcf_callaux_t *bca = 0;
bcf_callret1_t *bcr = 0;
bcf_call_t bc;
bcf_t *bp = 0;
bcf_hdr_t *bh = 0;
bam_sample_t *sm = 0;
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(void*));
plp = calloc(n, sizeof(void*));
n_plp = calloc(n, sizeof(int*));
sm = bam_smpl_init();
// read the header and initialize data
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
if ( !data[i]->fp )
{
fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
exit(1);
}
data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
if ( !h_tmp ) {
fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
exit(1);
}
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
int beg, end;
bam_index_t *idx;
idx = bam_index_load(fn[i]);
if (idx == 0) {
fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
exit(1);
}
if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
fprintf(stderr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]);
exit(1);
}
if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
data[i]->iter = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
if (i == 0) h = h_tmp;
else {
// FIXME: to check consistency
bam_header_destroy(h_tmp);
}
}
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(void*));
//fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
// write the VCF header
if (conf->flag & MPLP_GLF) {
kstring_t s;
bh = calloc(1, sizeof(bcf_hdr_t));
s.l = s.m = 0; s.s = 0;
/* bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
for (i = 0; i < h->n_targets; ++i) {
kputs(h->target_name[i], &s);
kputc('\0', &s);
}
*/ bh->l_nm = s.l;
bh->name = malloc(s.l);
memcpy(bh->name, s.s, s.l);
s.l = 0;
/* for (i = 0; i < sm->n; ++i) {
kputs(sm->smpl[i], &s); kputc('\0', &s);
}
*/ bh->l_smpl = s.l;
bh->sname = malloc(s.l);
memcpy(bh->sname, s.s, s.l);
s.l = 0;
// ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
// if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
h->dict = sam_header_parse2(h->text);
int nseq;
const char *tags[] = {"SN","LN","UR","M5",NULL};
char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
/* for (i=0; i<nseq; i++)
{
ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
kputs(">\n", &s);
}
*/ if (tbl) free(tbl);
bh->txt = s.s;
bh->l_txt = 1 + s.l;
// bcf_hdr_sync(bh);
// bcf_hdr_write(bp, bh);
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;
}
if (tid0 >= 0 && conf->fai) { // region is set
ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
ref_tid = tid0;
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
} else ref_tid = -1, ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
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);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
if (tid != ref_tid) {
free(ref); ref = 0;
if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
ref_tid = tid;
}
if (conf->flag & MPLP_GLF) {
int total_depth, _ref0, ref16;
// bcf1_t *b = calloc(1, sizeof(bcf1_t));
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 = bam_nt16_table[_ref0];
// call indels
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) {
printf("%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;
if (bam1_qual(p->b)[p->qpos] == 0){bam1_qual(p->b)[p->qpos] = conf->min_baseQ;}
if ((bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)) ++cnt;
}
printf("\t%d\t", cnt);
if (n_plp[i] == 0) {
printf("*\t*"); // FIXME: printf() is very slow...
if (conf->flag & MPLP_PRINT_POS) printf("\t*");
} else {
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if ((bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)){
pileup_seq(plp[i] + j, pos, ref_len, ref);
// printf("%s",bam1_qname(p->b));putchar('|');
}
}
if (conf->flag & MPLP_PRINT_POS) {
putchar('\t');
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if ((j >= 0) & (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)) {
putchar(',');
// printf("%s",bam1_qname(p->b));putchar('|');
printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
}
}
}
/* if (conf->flag & MPLP_PRINT_POS) {
putchar('\t');
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if ((j >= 0) & (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)){
putchar(',');
// printf("%s",bam1_qname(p->b));putchar('|');
printf("%d", plp[i][j].b->core.l_qseq); // FIXME: printf() is very slow...
}
}
}
//print qname
if (conf->flag & MPLP_PRINT_POS) {
putchar('\t');
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if ((j >= 0) & (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)){
putchar(',');
printf("%s",bam1_qname(p->b));putchar('|');
}
}
}
*/
// print CIGAR
if (conf->flag & MPLP_PRINT_POS) {
putchar('\t');
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if ((j >= 0) & (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) & (plp[i][j].b->core.qual >= conf->min_mq)){
putchar(',');
uint32_t *cigar = bam1_cigar(p->b);
int k;
for (k = 0; k < p->b->core.n_cigar; ++k){
printf("%d",bam_cigar_oplen(cigar[k]));
printf("%c",bam_cigar_opchr(cigar[k]));
}
}
}
}
}
}
putchar('\n');
}
}
}
bcf_close(bp);
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);
bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
bam_mplp_destroy(iter);
bam_header_destroy(h);
for (i = 0; i < n; ++i) {
bam_close(data[i]->fp);
if (data[i]->iter) bam_iter_destroy(data[i]->iter);
free(data[i]);
}
free(data); free(plp); free(ref); free(n_plp);
return 0;
}
#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 (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 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.max_mq = 60;
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;
static struct option lopts[] =
{
{"rf",1,0,1}, // require flag
{"ff",1,0,2}, // filter flag
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
switch (c) {
case 1 : mplp.rflag_require = strtol(optarg,0,0); break;
case 2 : mplp.rflag_filter = strtol(optarg,0,0); break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
mplp.fai_fname = optarg;
break;
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.bed = bed_read(optarg); break;
case 'P': mplp.pl_list = strdup(optarg); break;
case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
case 'g': mplp.flag |= MPLP_GLF; break;
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'B': mplp.flag &= ~MPLP_REALN; break;
case 'D': mplp.fmt_flag |= B2B_FMT_DP; break;
case 'S': mplp.fmt_flag |= B2B_FMT_SP; break;
case 'V': mplp.fmt_flag |= B2B_FMT_DV; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
case '6': mplp.flag |= MPLP_ILLUMINA13; break;
case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
case 'O': mplp.flag |= MPLP_PRINT_POS; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;
case 'b': file_list = optarg; break;
case 'o': mplp.openQ = atoi(optarg); break;
case 'e': mplp.extQ = atoi(optarg); break;
case 'h': mplp.tandemQ = atoi(optarg); break;
case 'A': use_orphan = 1; break;
case 'F': mplp.min_frac = atof(optarg); break;
case 'm': mplp.min_support = atoi(optarg); break;
case 'L': mplp.max_indel_depth = atoi(optarg); break;
case 'G': {
FILE *fp_rg;
char buf[1024];
mplp.rghash = bcf_str2id_init();
if ((fp_rg = fopen(optarg, "r")) == 0)
fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
bcf_str2id_add(mplp.rghash, strdup(buf));
fclose(fp_rg);
}
break;
}
}
if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
if (argc == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
fprintf(stderr, "Input options:\n\n");
fprintf(stderr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
fprintf(stderr, " -A count anomalous read pairs\n");
fprintf(stderr, " -B disable BAQ computation\n");
fprintf(stderr, " -b FILE list of input BAM filenames, one per line [null]\n");
fprintf(stderr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
fprintf(stderr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
fprintf(stderr, " -E recalculate extended BAQ on the fly thus ignoring existing BQs\n");
fprintf(stderr, " -f FILE faidx indexed reference sequence file [null]\n");
fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
fprintf(stderr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
fprintf(stderr, " -R ignore RG tags\n");
fprintf(stderr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(stderr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
fprintf(stderr, " --rf INT required flags: skip reads with mask bits unset []\n");
fprintf(stderr, " --ff INT filter flags: skip reads with mask bits set []\n");
fprintf(stderr, "\nOutput options:\n\n");
fprintf(stderr, " -D output per-sample DP in BCF (require -g/-u)\n");
fprintf(stderr, " -g generate BCF output (genotype likelihoods)\n");
fprintf(stderr, " -O output base positions on reads (disabled by -g/-u)\n");
fprintf(stderr, " -s output mapping quality (disabled by -g/-u)\n");
fprintf(stderr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
fprintf(stderr, " -u generate uncompress BCF output\n");
fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
fprintf(stderr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
fprintf(stderr, " -I do not perform indel calling\n");
fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
fprintf(stderr, " -p apply -m and -F per-sample to increase sensitivity\n");
fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;
}
bam_no_B = 1;
if (file_list) {
if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
mpileup(&mplp,nfiles,fn);
for (c=0; c<nfiles; c++) free(fn[c]);
free(fn);
} else mpileup(&mplp, argc - optind, argv + optind);
if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
free(mplp.reg); free(mplp.pl_list);
if (mplp.fai) fai_destroy(mplp.fai);
if (mplp.bed) bed_destroy(mplp.bed);
return 0;
}
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