When -B is applied to mpileup, still use paired reads only unless -A is flagged.

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 591257b9c7c119f51267bdbcdeda8ff96865a590..7e72b4e8f67e012747925c7302cea05c031f8a80 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.10-2 (r832)"
+#define PACKAGE_VERSION "0.1.12-7 (r888)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -95,6 +95,12 @@ static int usage()
        fprintf(stderr, "         rmdup       remove PCR duplicates\n");
        fprintf(stderr, "         reheader    replace BAM header\n");
        fprintf(stderr, "\n");
+#ifdef _WIN32
+       fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+      operations, such as viewing the alignments and generating the pileup.\n\
+      Binary files generated by the Windows version may be buggy.\n\n");
+#endif
        return 1;
 }