Merge commit 'upstream/0.1.10'

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 3386836e04e3a0b44eb47ff9d925d0db20b8ea90..88328d47c24fc6bfe6f602ffce721fb4ee64e56c 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -1,26 +1,32 @@
 #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 "0.1.5c (r385)"
+#define PACKAGE_VERSION "0.1.10 (r829)"
 #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[]);
@@ -71,43 +77,55 @@ static int usage()
        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 {