#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-22 (r432)"
+#define PACKAGE_VERSION "0.1.6 (r453)"
#endif
int bam_taf2baf(int argc, char *argv[]);
fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
fprintf(stderr, "Usage: samtools <command> [options]\n\n");
- fprintf(stderr, "Command: import import from SAM (obsolete; use `view')\n");
- fprintf(stderr, " view export to the text format\n");
+ fprintf(stderr, "Command: view SAM<->BAM conversion\n");
fprintf(stderr, " sort sort alignment file\n");
- fprintf(stderr, " merge merge multiple sorted alignment files\n");
fprintf(stderr, " pileup generate pileup output\n");
fprintf(stderr, " faidx index/extract FASTA\n");
#if _CURSES_LIB != 0
#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 GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
- fprintf(stderr, " fillmd recalculate MD/NM tags and '=' bases\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, "\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], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);