#include <stdio.h>
#include <unistd.h>
+#include <assert.h>
+#include <fcntl.h>
#include "bam.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-27"
+#define PACKAGE_VERSION "0.1.6-3 (r458)"
#endif
int bam_taf2baf(int argc, char *argv[]);
int bam_tview_main(int argc, char *argv[]);
int bam_mating(int argc, char *argv[]);
int bam_rmdup(int argc, char *argv[]);
+int bam_rmdupse(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
-static int view_aux(const bam1_t *b, void *data)
+int bam_tagview(int argc, char *argv[])
{
- bam_view1((bam_header_t*)data, b);
- return 0;
-}
-static int view_auxb(const bam1_t *b, void *data)
-{
- bam_write1((bamFile)data, b);
- return 0;
-}
-
-int bam_view(int argc, char *argv[])
-{
- bamFile fp, fpout = 0;
+ bamFile fp;
bam_header_t *header;
bam1_t *b;
- int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
- while ((c = getopt(argc, argv, "bhH")) >= 0) {
- switch (c) {
- case 'b': is_bam = 1; break;
- case 'h': is_header = 1; break;
- case 'H': is_headeronly = 1; break;
- default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
- }
- }
- if (argc == optind) {
- fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
+ char tag[2];
+ int ret;
+ if (argc < 3) {
+ fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
return 1;
}
- fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
assert(fp);
header = bam_header_read(fp);
- if (is_bam) {
- assert(fpout = bam_dopen(fileno(stdout), "w"));
- bam_header_write(fpout, header);
- }
- if (is_header || is_headeronly) {
- int i, c;
- c = header->text[header->l_text-1];
- header->text[header->l_text-1] = 0;
- printf("%s", header->text);
- if (c) putchar(c);
- header->text[header->l_text-1] = c;
- for (i = 0; i < header->n_targets; ++i)
- printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
- if (is_headeronly) {
- bam_header_destroy(header);
- bam_close(fp);
- return 0;
- }
+ if (header == 0) {
+ fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
+ return 1;
}
- if (optind + 1 == argc) {
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
- while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
- if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
- free(b->data); free(b);
- } else {
- int i;
- bam_index_t *idx;
- idx = bam_index_load(argv[optind]);
- for (i = optind + 1; i < argc; ++i) {
- int tid, beg, end;
- bam_parse_region(header, argv[i], &tid, &beg, &end);
- if (tid < 0) return 0;
- if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
- else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
+ tag[0] = argv[2][0]; tag[1] = argv[2][1];
+ b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ uint8_t *d = bam_aux_get(b, tag);
+ if (d) {
+ printf("%s\t%d\t", bam1_qname(b), b->core.flag);
+ if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
+ else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
+ else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
+ else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
+ else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
+ else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
+ else printf("\n");
}
- bam_index_destroy(idx);
}
+ if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
+ free(b->data); free(b);
bam_header_destroy(header);
bam_close(fp);
- if (is_bam) bam_close(fpout);
return 0;
}
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 the text format\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, " pileup generate pileup output\n");
fprintf(stderr, " faidx index/extract FASTA\n");
-#ifndef _NO_CURSES
+#if _CURSES_LIB != 0
fprintf(stderr, " tview text alignment viewer\n");
#endif
fprintf(stderr, " index index alignment\n");
fprintf(stderr, " fixmate fix mate information\n");
- fprintf(stderr, " rmdup remove PCR duplicates\n");
- fprintf(stderr, " glfview print GLFv2 file\n");
+ fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
+ fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
+ fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
fprintf(stderr, "\n");
return 1;
}
int main(int argc, char *argv[])
{
+#ifdef _WIN32
+ setmode(fileno(stdout), O_BINARY);
+ setmode(fileno(stdin), O_BINARY);
+#ifdef _USE_KNETFILE
+ knet_win32_init();
+#endif
+#endif
if (argc < 2) return usage();
- if (strcmp(argv[1], "view") == 0) return bam_view(argc-1, argv+1);
- else if (strcmp(argv[1], "import") == 0) return bam_taf2baf(argc-1, argv+1);
+ if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
+ else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
+ else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+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);
-#ifndef _NO_CURSES
+ 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);
#endif
else {
projects / samtools.git / blobdiff