From b2f01dc801f42b4d0372a3f0806472168c772956 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Thu, 19 Dec 2013 13:26:31 -0500
Subject: [PATCH] Added -nobuf option and definition to intersect help menu.
---
src/intersectFile/intersectMain.cpp | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
index 4aac270a..0e032f94 100644
--- a/src/intersectFile/intersectMain.cpp
+++ b/src/intersectFile/intersectMain.cpp
@@ -110,7 +110,15 @@ void intersect_help(void) {
cerr <<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl;
cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
-
+
+ cerr << "\t-nobuf\t" << "Disable buffered output. Using this option will cause each line"<< endl;
+ cerr <<"\t\tof output to be printed as it is generated, rather than saved" << endl;
+ cerr <<"\t\tin a buffer. This will make printing large output files " << endl;
+
+ cerr <<"\t\tnoticeably slower, but can be useful in conjunction with" << endl;
+ cerr <<"\t\tother software tools and scripts that need to process one" << endl;
+ cerr <<"\t\tline of bedtools output at a time." << endl << endl;
+
cerr << "Notes: " << endl;
cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
--
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