X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=8ba25811d2771e171fa08899015449618838f265;hb=3384f6c6c1642ada4edae9204ca1202672de7d5a;hp=79b0dbca368c4c00df6400ae207f28885074ea5d;hpb=4d48006473298b62ee54f13d706f9f2e512e02bd;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 79b0dbc..8ba2581 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -26,6 +26,7 @@ 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 main_bam2fq(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 
@@ -92,6 +93,11 @@ int main(int argc, char *argv[])
 	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);
+	else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(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;
+	}
 #if _CURSES_LIB != 0
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif