#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6-10 (r474)"
+#define PACKAGE_VERSION "0.1.7-9 (r586)"
#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_rmdupse(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
- fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
- fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
+ fprintf(stderr, " merge merge sorted alignments\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " reheader replace BAM header\n");
fprintf(stderr, "\n");
return 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], "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], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif