X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bamtk.c;h=5886570a88f9fbdc43e6442f1f76df7f9e100243;hp=1d1151973fb08efbbb6d642480712fbc6b3b1563;hb=0242bdf14e88f1058887598cbf898c0d0af01a82;hpb=1539c893f863596db71ab2af75a802e935496940

diff --git a/bamtk.c b/bamtk.c
index 1d11519..5886570 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -25,6 +25,8 @@ int main_import(int argc, char *argv[]);
 int main_reheader(int argc, char *argv[]);
 int main_cut_target(int argc, char *argv[]);
 int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
@@ -79,6 +81,7 @@ static int usage()
 	fprintf(stderr, "         sort        sort alignment file\n");
 	fprintf(stderr, "         pileup      generate pileup output\n");
 	fprintf(stderr, "         mpileup     multi-way pileup\n");
+	fprintf(stderr, "         depth       compute the depth\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
 #if _CURSES_LIB != 0
 	fprintf(stderr, "         tview       text alignment viewer\n");
@@ -92,6 +95,7 @@ static int usage()
 	fprintf(stderr, "         merge       merge sorted alignments\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "         reheader    replace BAM header\n");
+	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, "\n");
@@ -131,8 +135,10 @@ int main(int argc, char *argv[])
 	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);
+	else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
 	else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
 	else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+	else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
 #if _CURSES_LIB != 0
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif