#include <stdio.h>
#include <unistd.h>
#include <ctype.h>
+#include <string.h>
+#include <errno.h>
#include "sam.h"
#include "faidx.h"
#include "bam_maqcns.h"
return hash;
}
+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;
+}
+
// 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)
{
return 0;
}
-static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
- if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+ int j;
+ if (p->is_head) {
+ putchar('^');
+ putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+ }
if (!p->is_del) {
- int j, rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
- rb = (ref && pos < ref_len)? ref[pos] : 'N';
- if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
- else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+ 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);
- 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 = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
- putchar(bam1_strand(p->b)? tolower(c) : toupper(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));
}
- } else putchar('*');
+ }
if (p->is_tail) putchar('$');
}
}
}
// print the first 3 columns
- printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
+ fputs(d->h->target_name[tid], stdout); putchar('\t');
+ printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
// print consensus information if required
- if (d->format & BAM_PLF_CNS)
- printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, cns&0xff, cns>>16&0xff);
- // 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;
- pileup_seq(p, pos, d->len, d->ref);
+ if (d->format & BAM_PLF_CNS) {
+ putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
+ printw(cns>>8&0xff, stdout); putchar('\t');
+ printw(cns&0xff, stdout); putchar('\t');
+ printw(cns>>16&0xff, stdout); putchar('\t');
}
+ // print pileup sequences
+ printw(n, stdout); putchar('\t');
+ for (i = 0; i < n; ++i)
+ pileup_seq(pu + i, pos, d->len, d->ref);
// finalize rms_mapq
- rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
- if (rms_mapq < 0) rms_mapq = rms_aux;
+ if (d->format & BAM_PLF_CNS) {
+ for (i = rms_aux = 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;
+ }
+ 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) {
for (i = 0; i < n; ++i) {
int x = pu[i].qpos;
int l = pu[i].b->core.l_qseq;
- printf("%d,", x < l/2? x+1 : -((l-1)-x+1));
+ printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
}
}
putchar('\n');
bam_plp_set_mask(iter, d->mask);
while ((ret = samread(fp, b)) >= 0) {
int skip = 0;
+ if ((int)b->core.tid < 0) break;
// update d->ref if necessary
if (d->fai && (int)b->core.tid != d->tid) {
free(d->ref);
#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN 0x80
+#define MPLP_FMT_DP 0x100
+#define MPLP_FMT_SP 0x200
typedef struct {
- int max_mq, min_mq, flag, min_baseQ, capQ_thres;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
char *reg, *fn_pos;
faidx_t *fai;
kh_64_t *hash;
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
mplp_aux_t **data;
- int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
+ int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
}
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-sample depth to %d\n", __func__, max_depth);
+ }
+ 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 (hash) {
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bcf_call_combine(gplp.n, bcr, ref16, &bc);
- bcf_call2bcf(tid, pos, &bc, b);
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
bcf_write(bp, bh, b);
bcf_destroy(b);
+ // test if there is an indel
+ if (conf->flag&MPLP_REALN) {
+ for (i = 0; i < gplp.n; ++i) {
+ int j;
+ for (j = 0; j < gplp.n_plp[i]; ++j) {
+ const bam_pileup1_t *p = gplp.plp[i] + j;
+ if (p->indel != 0) break;
+ }
+ if (j != gplp.n_plp[i]) break;
+ }
+ if (i < gplp.n) { // at least one of the read contains a gap
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i);
+ bcf_call_combine_gap(gplp.n, bcr, &bc);
+ if (bc.depth > 0) {
+ b = calloc(1, sizeof(bcf1_t));
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP));
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ }
+ }
+ }
} else {
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) {
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;
+ char **files;
+
+ FILE *fh = fopen(file_list,"r");
+ if ( !fh )
+ {
+ fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+ return 1;
+ }
+
+ // Speed is not an issue here, determine the number of files by reading the file twice
+ nfiles = 0;
+ while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++;
+
+ if ( fseek(fh, 0L, SEEK_SET) )
+ {
+ 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) )
+ {
+ len = strlen(buf);
+ while ( len>0 && isspace(buf[len-1]) ) len--;
+ if ( !len ) continue;
+
+ files[nfiles] = malloc(sizeof(char)*(len+1));
+ strncpy(files[nfiles],buf,len);
+ files[nfiles][len] = 0;
+ nfiles++;
+ }
+ 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;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
+ mplp.max_depth = 250;
+ mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
break;
+ case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); 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 & ~MPLP_NO_ORPHAN; break;
case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
case 'R': mplp.flag |= MPLP_REALN; break;
+ case 'D': mplp.flag |= MPLP_FMT_DP; break;
+ case 'S': mplp.flag |= MPLP_FMT_SP; 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;
}
}
if (argc == 1) {
fprintf(stderr, "Options: -f FILE reference sequence file [null]\n");
fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n");
+ fprintf(stderr, " -b FILE list of input BAM files [null]\n");
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(stderr, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
+ fprintf(stderr, " -B disable BAQ computation\n");
+ fprintf(stderr, " -D output per-sample DP\n");
+ fprintf(stderr, " -S output per-sample SP (strand bias P-value, slow)\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;
}
- mpileup(&mplp, argc - optind, argv + optind);
+ 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);
free(mplp.reg);
if (mplp.fai) fai_destroy(mplp.fai);
return 0;
projects / samtools.git / blobdiff