#include <string.h>
#include <stdio.h>
#include <unistd.h>
+#include <math.h>
+#include "sam_header.h"
#include "sam.h"
+#include "faidx.h"
+#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;
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
static char *g_library, *g_rg;
+static int g_sol2sanger_tbl[128];
+
+static void sol2sanger(bam1_t *b)
+{
+ int l;
+ uint8_t *qual = bam1_qual(b);
+ if (g_sol2sanger_tbl[30] == 0) {
+ for (l = 0; l != 128; ++l) {
+ g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
+ if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
+ }
+ }
+ for (l = 0; l < b->core.l_qseq; ++l) {
+ int q = qual[l];
+ if (q > 127) q = 127;
+ qual[l] = g_sol2sanger_tbl[q];
+ }
+}
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) {
+ if (g_rg || g_rghash) {
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 = bam_strmap_get(h->rg2lib, (char*)(s + 1));
- return (p && strcmp(p, g_library) == 0)? 0 : 1;
- } return 1;
- } else return 1;
- } else return 0;
+ if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
+ if (g_rghash) {
+ khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
+ return (k != kh_end(g_rghash))? 0 : 1;
+ }
+ }
+ }
+ if (g_library) {
+ const char *p = bam_get_library((bam_header_t*)h, b);
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ }
+ 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;
}
-static int usage(void);
+// 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;
+ 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;
+ 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:")) >= 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;
case 't': fn_list = strdup(optarg); is_bamin = 0; break;
case 'u': is_uncompressed = 1; break;
case 'l': g_library = strdup(optarg); break;
case 'r': g_rg = strdup(optarg); break;
- default: return usage();
+ case 'R': fn_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 (is_uncompressed) strcat(out_mode, "u");
- if (argc == optind) return usage();
+ if (argc == optind) return usage(is_long_help); // potential memory leak...
+
+ // read the list of read groups
+ if (fn_rg) {
+ FILE *fp_rg;
+ char buf[1024];
+ int ret;
+ g_rghash = kh_init(rg);
+ fp_rg = fopen(fn_rg, "r");
+ while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
+ kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
+ fclose(fp_rg);
+ }
+ // 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");
+ fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
+ ret = 1;
+ goto view_end;
+ }
+ if (in->header == 0) {
+ fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
+ ret = 1;
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");
+ 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;
}
if (is_header_only) goto view_end; // no need to print alignments
if (argc == optind + 1) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
- while ((r = samread(in, b)) >= 0) // read one alignment from `in'
- 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");
+ while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
+ if (!__g_skip_aln(in->header, b)) {
+ if (slx2sngr) sol2sanger(b);
+ if (!is_count) samwrite(out, b); // write the alignment to `out'
+ count++;
+ }
+ }
+ if (r < -1) {
+ fprintf(stderr, "[main_samview] truncated file.\n");
+ ret = 1;
+ }
bam_destroy1(b);
} else { // retrieve alignments in specified regions
int i;
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] fail to get the reference name. Continue anyway.\n");
+ fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
continue;
}
- bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
+ // fetch alignments
+ 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;
+ }
}
bam_index_destroy(idx); // destroy the BAM index
}
view_end:
+ if (is_count && ret == 0) {
+ printf("%d\n", count);
+ }
// close files, free and return
- free(fn_list); free(fn_out); free(g_library); free(g_rg);
+ free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+ if (g_rghash) {
+ khint_t k;
+ for (k = 0; k < kh_end(g_rghash); ++k)
+ if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
+ kh_destroy(rg, g_rghash);
+ }
samclose(in);
- samclose(out);
+ if (!is_count)
+ 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, " -H print header only (no alignments)\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, " -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");
+ fprintf(stderr, " -R FILE list of read groups to be outputted [null]\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, " -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, "\n\
-Notes:\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\
\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