From 966318913a43d32c7d01ecf936325068ffddfdef Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 21 Sep 2010 09:43:20 -0400
Subject: [PATCH] bamToBed assumes stdin.
---
src/bamToBed/bamToBed.cpp | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index 154cbfc3..6758e126 100644
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -55,11 +55,11 @@ int main(int argc, char* argv[]) {
bool showHelp = false;
// input files
- string bamFile;
- string color = "255,0,0";
- string tag = "";
+ string bamFile = "stdin";
+ string color = "255,0,0";
+ string tag = "";
- bool haveBam = false;
+ bool haveBam = true;
bool haveColor = false;
bool haveOtherTag = false;
bool writeBedPE = false;
@@ -69,7 +69,6 @@ int main(int argc, char* argv[]) {
bool obeySplits = false;
// check to see if we should print out some help
- if(argc <= 1) showHelp = true;
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -89,7 +88,6 @@ int main(int argc, char* argv[]) {
if(PARAMETER_CHECK("-i", 2, parameterLength)) {
if ((i+1) < argc) {
- haveBam = true;
bamFile = argv[i + 1];
i++;
}
--
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