From: Heng Li <lh3@me.com>
Date: Tue, 17 Apr 2012 20:03:11 +0000 (-0400)
Subject: r572: added "bedcov" command
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=fa6c5588e0d3845a98ea54435d49ccbe305515d7;p=samtools.git
r572: added "bedcov" command
---
diff --git a/Makefile b/Makefile
index 6ddd4dd..4a8a75b 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,7 @@ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
- cut_target.o phase.o bam2depth.o padding.o
+ cut_target.o phase.o bam2depth.o padding.o bedcov.o
PROG= samtools
INCLUDES= -I.
SUBDIRS= . bcftools misc
diff --git a/bam.h b/bam.h
index efc0459..82f1ffa 100644
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.18-master-r567"
+#define BAM_VERSION "0.1.18-r572"
#include <stdint.h>
#include <stdlib.h>
diff --git a/bamtk.c b/bamtk.c
index 2e7fcb0..acdf65f 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -28,6 +28,7 @@ int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
int main_bam2fq(int argc, char *argv[]);
int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
@@ -54,6 +55,7 @@ static int usage()
fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " reheader replace BAM header\n");
fprintf(stderr, " cat concatenate BAMs\n");
+ fprintf(stderr, " bedcov read depth per BED region\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
// fprintf(stderr, " depad convert padded BAM to unpadded BAM\n"); // not stable
@@ -98,6 +100,7 @@ int main(int argc, char *argv[])
else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "depad") == 0) return main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "bedcov") == 0) return main_bedcov(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
diff --git a/bedcov.c b/bedcov.c
new file mode 100644
index 0000000..2b61a22
--- /dev/null
+++ b/bedcov.c
@@ -0,0 +1,126 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include "kstring.h"
+#include "bgzf.h"
+#include "bam.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+typedef struct {
+ bamFile fp;
+ bam_iter_t iter;
+ int min_mapQ;
+} aux_t;
+
+static int read_bam(void *data, bam1_t *b)
+{
+ aux_t *aux = (aux_t*)data;
+ int ret = bam_iter_read(aux->fp, aux->iter, b);
+ if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ return ret;
+}
+
+int main_bedcov(int argc, char *argv[])
+{
+ extern void bam_init_header_hash(bam_header_t*);
+ gzFile fp;
+ kstring_t str;
+ kstream_t *ks;
+ bam_index_t **idx;
+ bam_header_t *h = 0;
+ aux_t **aux;
+ int *n_plp, dret, i, n, c, min_mapQ = 0;
+ int64_t *cnt;
+ const bam_pileup1_t **plp;
+
+ while ((c = getopt(argc, argv, "Q:")) >= 0) {
+ switch (c) {
+ case 'Q': min_mapQ = atoi(optarg); break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "Usage: samtools bedcov <in.bed> <in1.bam> [...]\n");
+ return 1;
+ }
+ memset(&str, 0, sizeof(kstring_t));
+ n = argc - optind - 1;
+ aux = calloc(n, sizeof(void*));
+ idx = calloc(n, sizeof(void*));
+ for (i = 0; i < n; ++i) {
+ aux[i] = calloc(1, sizeof(aux_t));
+ aux[i]->min_mapQ = min_mapQ;
+ aux[i]->fp = bam_open(argv[i+optind+1], "r");
+ idx[i] = bam_index_load(argv[i+optind+1]);
+ if (aux[i]->fp == 0 || idx[i] == 0) {
+ fprintf(stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
+ return 2;
+ }
+ bgzf_set_cache_size(aux[i]->fp, 20);
+ if (i == 0) h = bam_header_read(aux[0]->fp);
+ }
+ bam_init_header_hash(h);
+ cnt = calloc(n, 8);
+
+ fp = gzopen(argv[optind], "rb");
+ ks = ks_init(fp);
+ n_plp = calloc(n, sizeof(int));
+ plp = calloc(n, sizeof(void*));
+ while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+ char *p, *q;
+ int tid, beg, end, pos;
+ bam_mplp_t mplp;
+
+ for (p = q = str.s; *p && *p != '\t'; ++p);
+ if (*p != '\t') goto bed_error;
+ *p = 0; tid = bam_get_tid(h, q); *p = '\t';
+ if (tid < 0) goto bed_error;
+ for (q = p = p + 1; isdigit(*p); ++p);
+ if (*p != '\t') goto bed_error;
+ *p = 0; beg = atoi(q); *p = '\t';
+ for (q = p = p + 1; isdigit(*p); ++p);
+ if (*p == '\t' || *p == 0) {
+ int c = *p;
+ *p = 0; end = atoi(q); *p = c;
+ } else goto bed_error;
+
+ for (i = 0; i < n; ++i) {
+ if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+ aux[i]->iter = bam_iter_query(idx[i], tid, beg, end);
+ }
+ mplp = bam_mplp_init(n, read_bam, (void**)aux);
+ bam_mplp_set_maxcnt(mplp, 64000);
+ memset(cnt, 0, 8 * n);
+ while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0)
+ if (pos >= beg && pos < end)
+ for (i = 0; i < n; ++i) cnt[i] += n_plp[i];
+ for (i = 0; i < n; ++i) {
+ kputc('\t', &str);
+ kputl(cnt[i], &str);
+ }
+ puts(str.s);
+ bam_mplp_destroy(mplp);
+ continue;
+
+bed_error:
+ fprintf(stderr, "Errors in BED line '%s'\n", str.s);
+ }
+ free(n_plp); free(plp);
+ ks_destroy(ks);
+ gzclose(fp);
+
+ free(cnt);
+ for (i = 0; i < n; ++i) {
+ if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+ bam_index_destroy(idx[i]);
+ bam_close(aux[i]->fp);
+ free(aux[i]);
+ }
+ bam_header_destroy(h);
+ free(aux); free(idx);
+ free(str.s);
+ return 0;
+}
diff --git a/kstring.h b/kstring.h
index d490f58..abd8236 100644
--- a/kstring.h
+++ b/kstring.h
@@ -142,6 +142,23 @@ static inline int kputuw(unsigned c, kstring_t *s)
return 0;
}
+static inline int kputl(long c, kstring_t *s)
+{
+ char buf[32];
+ long l, x;
+ if (c == 0) return kputc('0', s);
+ for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (c < 0) buf[l++] = '-';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+ s->s[s->l] = 0;
+ return 0;
+}
+
static inline int *ksplit(kstring_t *s, int delimiter, int *n)
{
int max = 0, *offsets = 0;