#include <string.h>
#include <stdio.h>
#include <unistd.h>
+#include "sam_header.h"
#include "sam.h"
+#include "faidx.h"
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static char *g_library, *g_rg;
+
+static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
+{
+ if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
+ return 1;
+ if (g_library || g_rg) {
+ uint8_t *s = bam_aux_get(b, "RG");
+ if (s) {
+ if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
+ if (g_library) {
+ const char *p = sam_tbl_get(h->rg2lib, (const char*)(s + 1));
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ } return 1;
+ } else return 1;
+ } else return 0;
+}
// callback function for bam_fetch()
static int view_func(const bam1_t *b, void *data)
{
- if (b->core.qual < g_min_mapQ) return 0;
- if (g_flag_on && (b->core.flag & g_flag_on) == 0) return 0;
- if (b->core.flag & g_flag_off) return 0;
- samwrite((samfile_t*)data, b);
+ if (!__g_skip_aln(((samfile_t*)data)->header, b))
+ samwrite((samfile_t*)data, b);
return 0;
}
-static int usage(void);
+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;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
+ int of_type = BAM_OFDEC, is_long_help = 0;
samfile_t *in = 0, *out = 0;
- char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "bt:hHo:q:f:F:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:")) >= 0) {
switch (c) {
- case 'b': strcat(out_mode, "b"); break;
+ case 'S': is_bamin = 0; break;
+ case 'b': is_bamout = 1; break;
case 't': fn_list = strdup(optarg); is_bamin = 0; break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'f': g_flag_on = strtol(optarg, 0, 0); break;
- case 'F': g_flag_on = strtol(optarg, 0, 0); break;
+ case 'F': g_flag_off = strtol(optarg, 0, 0); break;
case 'q': g_min_mapQ = atoi(optarg); break;
- default: return usage();
+ case 'u': is_uncompressed = 1; break;
+ case 'l': g_library = strdup(optarg); break;
+ case 'r': g_rg = strdup(optarg); break;
+ case 'x': of_type = BAM_OFHEX; break;
+ case 'X': of_type = BAM_OFSTR; break;
+ case '?': is_long_help = 1; break;
+ case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+ default: return usage(is_long_help);
}
}
+ if (is_uncompressed) is_bamout = 1;
if (is_header_only) is_header = 1;
+ if (is_bamout) strcat(out_mode, "b");
+ else {
+ if (of_type == BAM_OFHEX) strcat(out_mode, "x");
+ else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
+ }
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
- if (argc == optind) return usage();
+ if (is_uncompressed) strcat(out_mode, "u");
+ if (argc == optind) return usage(is_long_help);
+ // generate the fn_list if necessary
+ if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
// open file handlers
if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
fprintf(stderr, "[main_samview] fail to open file for reading.\n");
goto view_end;
}
+ if (in->header == 0) {
+ fprintf(stderr, "[main_samview] fail to read the header.\n");
+ goto view_end;
+ }
if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
fprintf(stderr, "[main_samview] fail to open file for writing.\n");
goto view_end;
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) // read one alignment from `in'
- samwrite(out, b); // write the alignment to `out'
+ if (!__g_skip_aln(in->header, b))
+ samwrite(out, b); // write the alignment to `out'
if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
bam_destroy1(b);
} else { // retrieve alignments in specified regions
view_end:
// close files, free and return
- free(fn_list); free(fn_out);
+ free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg);
samclose(in);
samclose(out);
return ret;
}
-static int usage()
+static int usage(int is_long_help)
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
fprintf(stderr, "Options: -b output BAM\n");
fprintf(stderr, " -h print header for the SAM output\n");
fprintf(stderr, " -H print header only (no alignments)\n");
- fprintf(stderr, " -t FILE list of reference names and lengths, assuming SAM input [null]\n");
+ fprintf(stderr, " -S input is SAM\n");
+ 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, " -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");
fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
fprintf(stderr, " -q INT minimum mapping quality [0]\n");
- fprintf(stderr, "\n\
-Notes:\n\
+ fprintf(stderr, " -l STR only output reads in library STR [null]\n");
+ fprintf(stderr, " -r STR only output reads in read group STR [null]\n");
+ fprintf(stderr, " -? longer help\n");
+ fprintf(stderr, "\n");
+ if (is_long_help)
+ fprintf(stderr, "Notes:\n\
\n\
1. By default, this command assumes the file on the command line is in\n\
the BAM format and it prints the alignments in SAM. If `-t' is\n\
corresponding sequence length. The `.fai' file generated by `faidx'\n\
can be used here. This file may be empty if reads are unaligned.\n\
\n\
- 2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
+ 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
\n\
3. BAM->SAM conversion: `samtools view in.bam'.\n\
\n\
4. A region should be presented in one of the following formats:\n\
`chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
specified, the input alignment file must be an indexed BAM file.\n\
+\n\
+ 5. Option `-u' is preferred over `-b' when the output is piped to\n\
+ another samtools command.\n\
+\n\
+ 6. In a string FLAG, each character represents one bit with\n\
+ p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
+ U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
+ 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
+ f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
+ `-X' are samtools-C specific. Picard and older samtools do not\n\
+ support HEX or string flags.\n\
\n");
return 1;
}
projects / samtools.git / blobdiff