#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 "0.1.4-4 (r325)"
+#define PACKAGE_VERSION "0.1.8-9 (r649)"
#endif
int bam_taf2baf(int argc, char *argv[]);
int bam_pileup(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
int bam_merge(int argc, char *argv[]);
int bam_index(int argc, char *argv[]);
int bam_sort(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 bam_idxstats(int argc, char *argv[]);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(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, " pileup generate pileup output\n");
+ fprintf(stderr, " mpileup multi-way pileup\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, " idxstats BAM index stats (r595 or later)\n");
fprintf(stderr, " fixmate fix mate information\n");
- fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
- fprintf(stderr, " fillmd fill the MD tag and change identical base to =\n");
+ fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " merge merge sorted alignments\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " reheader replace BAM header\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 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], "mpileup") == 0) return bam_mpileup(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], "index") == 0) return bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(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);
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);
-#ifndef _NO_CURSES
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(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 {