From a1f44cf7f1e6bcca5a415123d811960ed509815a Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 6 Jun 2012 13:04:42 -0400
Subject: [PATCH] -wo -wao -c with -abam force BED output. Thanks to @agordon.
---
src/intersectBed/intersectMain.cpp | 13 +++----------
1 file changed, 3 insertions(+), 10 deletions(-)
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index c26aae08..f1d26a24 100644
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -225,16 +225,9 @@ int intersect_main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****WARNING: -loj is ignored with -abam" << endl << "*****" << endl;
}
- if (inputIsBam && writeCount) {
- cerr << endl << "*****" << endl << "*****WARNING: -c is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (inputIsBam && writeOverlap) {
- cerr << endl << "*****" << endl << "*****WARNING: -wo is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (inputIsBam && writeAllOverlap) {
- cerr << endl << "*****" << endl << "*****WARNING: -wao is ignored with -abam" << endl << "*****" << endl;
+ if (outputIsBam && (writeCount || writeOverlap || writeAllOverlap))
+ {
+ outputIsBam = false;
}
if (!showHelp) {
--
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