X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=2e7fcb0a522f2c7ae8d6b190f4026f5fbda00bb1;hb=543a9fc2055575dcc17a7bb9c83ecca17a32cec6;hp=6700b55a4e496cac8d7bcb88c1119016adbd3e09;hpb=8d24fb5fbc6af6b2cff371641681a5dec2fe6616;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 6700b55..2e7fcb0 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -56,7 +56,7 @@ static int usage()
 	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, "\
@@ -97,6 +97,7 @@ int main(int argc, char *argv[])
 	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;