#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.1-18"
+#define PACKAGE_VERSION "0.1.2-10"
#endif
int bam_taf2baf(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[]);
for (i = optind + 1; i < argc; ++i) {
int tid, beg, end;
bam_parse_region(header, argv[i], &tid, &beg, &end);
+ if (tid < 0) return 0;
if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
}
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], "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