fprintf(stderr, " cat concatenate BAMs\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
- fprintf(stderr, " pad2unpad convert padded BAM to unpadded BAM\n");
+// fprintf(stderr, " depad convert padded BAM to unpadded BAM\n"); // not stable
fprintf(stderr, "\n");
#ifdef _WIN32
fprintf(stderr, "\
else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "depad") == 0) return main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;