#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.1"
+#define PACKAGE_VERSION "0.1.2-1"
#endif
int bam_taf2baf(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_flagstat(int argc, char *argv[]);
+
int faidx_main(int argc, char *argv[]);
+int glf_view_main(int argc, char *argv[]);
static int view_aux(const bam1_t *b, void *data)
{
fprintf(stderr, " tview text alignment viewer\n");
#endif
fprintf(stderr, " index index alignment\n");
+ fprintf(stderr, " fixmate fix mate information\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " glfview print GLFv2 file\n");
+ fprintf(stderr, " flagstat simple stats\n");
fprintf(stderr, "\n");
return 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], "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], "glfview") == 0) return glf_view_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
#ifndef _NO_CURSES
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif