X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=9df7c118ef595ba48f1b6760aafad84300ed18dd;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=acdf65fed3868ca1f934081b3af1b01536abe55f;hpb=c560dcebed800084f30f3c277d13e6fd8629908c;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index acdf65f..9df7c11 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -29,6 +29,7 @@ int main_depth(int argc, char *argv[]);
 int main_bam2fq(int argc, char *argv[]);
 int main_pad2unpad(int argc, char *argv[]);
 int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 
@@ -58,6 +59,7 @@ static int usage()
 	fprintf(stderr, "         bedcov      read depth per BED region\n");
 	fprintf(stderr, "         targetcut   cut fosmid regions (for fosmid pool only)\n");
 	fprintf(stderr, "         phase       phase heterozygotes\n");
+	fprintf(stderr, "         bamshuf     shuffle and group alignments by name\n");
 //	fprintf(stderr, "         depad       convert padded BAM to unpadded BAM\n"); // not stable
 	fprintf(stderr, "\n");
 #ifdef _WIN32
@@ -101,6 +103,7 @@ int main(int argc, char *argv[])
 	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], "bedcov") == 0) return main_bedcov(argc-1, argv+1);
+	else if (strcmp(argv[1], "bamshuf") == 0) return main_bamshuf(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;