X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=fb000a6425f3ea7246d6273e73d0f74cb6701166;hb=a5a8f24beaa6b65b40f29d89a62cf2c643100c6d;hp=a7e75cb59c9820201fd670fe0f570819acb7117f;hpb=f1222861f3824c28d35cd143f5565ca09d80f056;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index a7e75cb..fb000a6 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 "0.1.3-11 (r258)"
+#define PACKAGE_VERSION "0.1.5-9 (r405)"
 #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");
@@ -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 {