if (old_nm) old_nm_i = bam_aux2i(old_nm);
if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
else if (nm != old_nm_i) {
- uint8_t *old_data = b->data;
fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
bam_aux_del(b, old_nm);
bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
{
bamFile in, out;
if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n");
+ fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n\n");
+ fprintf(stderr, "Note: Picard is recommended for this task.\n");
return 1;
}
in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
samfile_t *in, *out;
buffer_t *buf;
if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdupse <in.bam> <out.bam>\n");
+ fprintf(stderr, "Usage: samtools rmdupse <in.bam> <out.bam>\n\n");
+ fprintf(stderr, "Note: Picard is recommended for this task.\n");
return 1;
}
buf = calloc(1, sizeof(buffer_t));
KSORT_INIT(heap, heap1_t, heap_lt)
+static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
+{
+ int tempi;
+ char *temps;
+ tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
+ temps = h1->text, h1->text = h2->text, h2->text = temps;
+}
+
/*!
@abstract Merge multiple sorted BAM.
@param is_by_qname whether to sort by query name
@param out output BAM file name
+ @param headers name of SAM file from which to copy '@' header lines,
+ or NULL to copy them from the first file to be merged
@param n number of files to be merged
@param fn names of files to be merged
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
+void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
+ bam_header_t *hheaders = NULL;
int i, j;
+ if (headers) {
+ tamFile fpheaders = sam_open(headers);
+ if (fpheaders == 0) {
+ fprintf(stderr, "[bam_merge_core] Cannot open file `%s'. Continue anyway.\n", headers);
+ } else {
+ hheaders = sam_header_read(fpheaders);
+ sam_close(fpheaders);
+ }
+ }
+
g_is_by_qname = by_qname;
fp = (bamFile*)calloc(n, sizeof(bamFile));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
bam_header_t *hin;
assert(fp[i] = bam_open(fn[i], "r"));
hin = bam_header_read(fp[i]);
- if (i == 0) hout = hin;
- else { // validate multiple baf
+ if (i == 0) { // the first SAM
+ hout = hin;
+ if (hheaders) {
+ // If the text headers to be swapped in include any @SQ headers,
+ // check that they are consistent with the existing binary list
+ // of reference information.
+ if (hheaders->n_targets > 0) {
+ if (hout->n_targets != hheaders->n_targets)
+ fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
+ for (j = 0; j < hout->n_targets; ++j)
+ if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0)
+ fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);
+ }
+ swap_header_text(hout, hheaders);
+ bam_header_destroy(hheaders);
+ hheaders = NULL;
+ }
+ } else { // validate multiple baf
if (hout->n_targets != hin->n_targets) {
fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
exit(1);
hout->target_name[j], hin->target_name[j], fn[i]);
exit(1);
}
- if (hout->target_len[j] != hin->target_len[j])
- fprintf(stderr, "[bam_merge_core] different target sequence length: %d != %d in file '%s'. Continue.\n",
- hout->target_len[j], hin->target_len[j], fn[i]);
}
bam_header_destroy(hin);
}
int bam_merge(int argc, char *argv[])
{
int c, is_by_qname = 0;
- while ((c = getopt(argc, argv, "n")) >= 0) {
+ char *fn_headers = NULL;
+
+ while ((c = getopt(argc, argv, "h:n")) >= 0) {
switch (c) {
+ case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
}
}
if (optind + 2 >= argc) {
- fprintf(stderr, "Usage: samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools merge [-n] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+ fprintf(stderr, "Options: -n sort by read names\n");
+ fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
+ fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
+ fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
+ fprintf(stderr, " the header dictionary in merging.\n\n");
return 1;
}
- bam_merge_core(is_by_qname, argv[optind], argc - optind - 1, argv + optind + 1);
+ bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1);
+ free(fn_headers);
return 0;
}
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
sprintf(fns[i], "%s.%.4d.bam", prefix, i);
}
- bam_merge_core(is_by_qname, fnout, n, fns);
+ bam_merge_core(is_by_qname, fnout, 0, n, fns);
free(fnout);
for (i = 0; i < n; ++i) {
-// unlink(fns[i]);
+ unlink(fns[i]);
free(fns[i]);
}
free(fns);
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-33 (r450)"
+#define PACKAGE_VERSION "0.1.5-34 (r451)"
#endif
int bam_taf2baf(int argc, char *argv[]);
fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
fprintf(stderr, "Usage: samtools <command> [options]\n\n");
- fprintf(stderr, "Command: import import from SAM (obsolete; use `view')\n");
- fprintf(stderr, " view export to the text format\n");
+ fprintf(stderr, "Command: view SAM<->BAM conversion\n");
fprintf(stderr, " sort sort alignment file\n");
- fprintf(stderr, " merge merge multiple sorted alignment files\n");
+ fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
fprintf(stderr, " pileup generate pileup output\n");
fprintf(stderr, " faidx index/extract FASTA\n");
#if _CURSES_LIB != 0
#endif
fprintf(stderr, " index index alignment\n");
fprintf(stderr, " fixmate fix mate information\n");
- fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
- fprintf(stderr, " fillmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
fprintf(stderr, "\n");
return 1;
}
else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
+ else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
pipes. Samtools always output warning and error messages to the standard
error output (stderr).
-Samtools is also able to open a BAM (not SAM) file on a remote FTP
-server if the BAM file name starts with `ftp://'. Samtools checks the
-current working directory for the index file and will download the index
-upon absence. Samtools achieves random FTP file access with the `REST'
-ftp command. It does not retrieve the entire alignment file unless it is
-asked to do so.
+Samtools is also able to open a BAM (not SAM) file on a remote FTP or
+HTTP server if the BAM file name starts with `ftp://' or `http://'.
+Samtools checks the current working directory for the index file and
+will download the index upon absence. Samtools does not retrieve the
+entire alignment file unless it is asked to do so.
.SH COMMANDS AND OPTIONS
.TP
.B merge
-samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]
-
-Merge multiple sorted alignments. The header of
-.I <in1.bam>
+samtools merge [-h inh.sam] [-n] <out.bam> <in1.bam> <in2.bam> [...]
+
+Merge multiple sorted alignments.
+The header reference lists of all the input BAM files, and the @SQ headers of
+.IR inh.sam ,
+if any, must all refer to the same set of reference sequences.
+The header reference list and (unless overridden by
+.BR -h )
+`@' headers of
+.I in1.bam
will be copied to
-.I <out.bam>
+.IR out.bam ,
and the headers of other files will be ignored.
.B OPTIONS:
.RS
.TP 8
+.B -h FILE
+Use the lines of
+.I FILE
+as `@' headers to be copied to
+.IR out.bam ,
+replacing any header lines that would otherwise be copied from
+.IR in1.bam .
+.RI ( FILE
+is actually in SAM format, though any alignment records it may contain
+are ignored.)
+.TP
.B -n
The input alignments are sorted by read names rather than by chromosomal
coordinates
Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
.IP o 2
CIGAR operation P is not properly handled at the moment.
+.IP o 2
+In merging, the input files are required to have the same number of
+reference sequences. The requirement can be relaxed. In addition,
+merging does not reconstruct the header dictionaries
+automatically. Endusers have to provide the correct header. Picard is
+better at merging.
+.IP o 2
+Samtools' rmdup does not work for single-end data and does not remove
+duplicates across chromosomes. Picard is better.
.SH AUTHOR
.PP
.SH SEE ALSO
.PP
-Samtools website: http://samtools.sourceforge.net
+Samtools website: <http://samtools.sourceforge.net>
projects / samtools.git / commitdiff