From 548bcae0db988318f72742f1cd5cdeeb43e9f951 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 25 Nov 2014 14:41:26 -0700
Subject: [PATCH] add -m option to merge intervals
---
src/fisher/fisherMain.cpp | 5 ++++-
src/utils/Contexts/ContextFisher.cpp | 4 ++++
2 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/src/fisher/fisherMain.cpp b/src/fisher/fisherMain.cpp
index d35b2868..584664e1 100644
--- a/src/fisher/fisherMain.cpp
+++ b/src/fisher/fisherMain.cpp
@@ -34,7 +34,7 @@ void fisher_help(void) {
cerr << "Summary: Calculate Fisher statistic b/w two feature files."
<< endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> -c <possible counts>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> -g <genome file>" << endl << endl;
cerr << "Options: " << endl;
@@ -43,6 +43,9 @@ void fisher_help(void) {
cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+ cerr << "\t-m\t" << "Merge overlapping intervals before" << endl;
+ cerr << "\t\t- looking at overlap." << endl << endl;
+
cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
diff --git a/src/utils/Contexts/ContextFisher.cpp b/src/utils/Contexts/ContextFisher.cpp
index fd00f982..2e9387dd 100644
--- a/src/utils/Contexts/ContextFisher.cpp
+++ b/src/utils/Contexts/ContextFisher.cpp
@@ -43,6 +43,10 @@ bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
if (strcmp(_argv[_i], "-g") == 0) {
if (!handle_g()) return false;
}
+ if(strcmp(_argv[_i], "-m") == 0) {
+ markUsed(_i - _skipFirstArgs);
+ setUseMergedIntervals(true);
+ }
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
--
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