X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=bamtk.c;h=f827aecb07dab38749212ccbadf80cbf6131e6c6;hb=2ec779405b1f89e1407c24956bbb3af584234bc9;hp=316b1285c0fb367a35f770cd39644ecfe8662a36;hpb=39cfa14f71a83dd06f77e4035852d975360d7a44;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 316b128..f827aec 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -1,9 +1,10 @@
 #include <stdio.h>
 #include <unistd.h>
+#include <assert.h>
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-14 (r262)"
+#define PACKAGE_VERSION "0.1.5-18 (r423)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -14,6 +15,7 @@ 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 +77,7 @@ 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");
@@ -83,7 +85,7 @@ 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;
 }
@@ -100,11 +102,12 @@ 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 {