Release samtools-0.1.17

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 79b0dbca368c4c00df6400ae207f28885074ea5d..8ba25811d2771e171fa08899015449618838f265 100644 (file)
--- 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