* samtools-0.1.5-24 (r435)

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 31ef17ce48343d9275aadecaca5d5268d8195ea1..0b41561eb37100de3244535d41069d9b8f4d3bfc 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -1,9 +1,15 @@
 #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 "0.1.3-15 (r266)"
+#define PACKAGE_VERSION "0.1.5-24 (r435)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -14,6 +20,7 @@ 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[]);
 
@@ -75,7 +82,7 @@ static int usage()
        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");
@@ -83,13 +90,20 @@ static int usage()
        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, "         fillmd      recalculate MD/NM tags and '=' bases\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);
@@ -100,11 +114,12 @@ int main(int argc, char *argv[])
        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], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
-#ifndef _NO_CURSES
+#if _CURSES_LIB != 0
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif
        else {