+------------------------------------------------------------------------
+r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r797)
+ * mpileup: indel calling seems to be working
+
+------------------------------------------------------------------------
+r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/kaln.c
+
+indel calling is apparently working, but more information needs to be collected
+
+------------------------------------------------------------------------
+r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf_indel.c
+
+fixed a few bugs in the indel caller. Probably there are more.
+
+------------------------------------------------------------------------
+r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ A /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+prepare for the indel caller. It is not ready yet.
+
+------------------------------------------------------------------------
+r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+Revert to r790. The recent changes are not good...
+
+------------------------------------------------------------------------
+r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+ * this revision is UNSTABLE
+
+ * indel caller seems working, but it is very insensitive and has
+ several things I do not quite understand.
+
+
+------------------------------------------------------------------------
+r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+for backup. no effective changes
+
+------------------------------------------------------------------------
+r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/kprobaln.c
+
+fixed a minor problem in the example coming with kprobaln.c
+
+------------------------------------------------------------------------
+r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+ A /trunk/samtools/kprobaln.c
+ A /trunk/samtools/kprobaln.h
+
+Separate kaln and kprobaln as I am preparing further changes. At
+present, the results should be identical to the previous.
+
+
+------------------------------------------------------------------------
+r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+Added -b option: read file names from a file
+------------------------------------------------------------------------
+r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r787)
+
+ * Allow to set a maximum per-sample depth to reduce memory. However,
+ BAQ computation is still applied to every read. The speed is not
+ improved.
+
+
+------------------------------------------------------------------------
+r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * samtools-0.1.9-1 (r786)
+ * samtools: optionally perform exact test for each sample
+
+------------------------------------------------------------------------
+r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bcftools/bcf.c
+
+Optionally output "DP", the individual read depth
+
+------------------------------------------------------------------------
+r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+acknowledge Petr and John who have greatly contributed to the project.
+
+------------------------------------------------------------------------
+r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.9 (r783)
+
------------------------------------------------------------------------
r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
Changed paths:
#include "khash.h"
KHASH_SET_INIT_STR(rg)
+// When counting records instead of printing them,
+// data passed to the bam_fetch callback is encapsulated in this struct.
+typedef struct {
+ bam_header_t *header;
+ int *count;
+} count_func_data_t;
+
typedef khash_t(rg) *rghash_t;
rghash_t g_rghash = 0;
return 0;
}
-// callback function for bam_fetch()
+// callback function for bam_fetch() that prints nonskipped records
static int view_func(const bam1_t *b, void *data)
{
if (!__g_skip_aln(((samfile_t*)data)->header, b))
return 0;
}
+// callback function for bam_fetch() that counts nonskipped records
+static int count_func(const bam1_t *b, void *data)
+{
+ if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+ (*((count_func_data_t*)data)->count)++;
+ }
+ return 0;
+}
+
static int usage(int is_long_help);
int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0, is_count = 0;
int of_type = BAM_OFDEC, is_long_help = 0;
+ int count = 0;
samfile_t *in = 0, *out = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
switch (c) {
+ case 'c': is_count = 1; break;
case 'C': slx2sngr = 1; break;
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
ret = 1;
goto view_end;
}
- if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+ if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
ret = 1;
goto view_end;
while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
if (!__g_skip_aln(in->header, b)) {
if (slx2sngr) sol2sanger(b);
- samwrite(out, b); // write the alignment to `out'
+ if (!is_count) samwrite(out, b); // write the alignment to `out'
+ count++;
}
}
if (r < -1) {
goto view_end;
}
for (i = optind + 1; i < argc; ++i) {
- int tid, beg, end;
+ int tid, beg, end, result;
bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
if (tid < 0) { // reference name is not found
fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
continue;
}
// fetch alignments
- if (bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func) < 0) {
+ if (is_count) {
+ count_func_data_t count_data = { in->header, &count };
+ result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
+ } else
+ result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
+ if (result < 0) {
fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
ret = 1;
break;
}
view_end:
+ if (is_count && ret == 0) {
+ printf("%d\n", count);
+ }
// close files, free and return
free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
if (g_rghash) {
kh_destroy(rg, g_rghash);
}
samclose(in);
- samclose(out);
+ if (!is_count)
+ samclose(out);
return ret;
}
fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
+ fprintf(stderr, " -c print only the count of matching records\n");
fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");