#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-2"
+#define PACKAGE_VERSION "0.1.3-3"
#endif
int bam_taf2baf(int argc, char *argv[]);
int bam_mating(int argc, char *argv[]);
int bam_rmdup(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " glfview print GLFv2 file\n");
fprintf(stderr, " flagstat simple stats\n");
+ fprintf(stderr, " fillmd fill the MD tag and change identical base to =\n");
fprintf(stderr, "\n");
return 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
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif