From 9628eca3ee28ece860518b28c0b29e9feb7926b6 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 14 Apr 2011 10:44:41 -0400
Subject: [PATCH] Tweaked Makefile and added notboth option to pairToPair.
---
Makefile | 2 --
src/pairToPair/pairToPair.cpp | 2 +-
src/pairToPair/pairToPair.h | 2 +-
src/pairToPair/pairToPairMain.cpp | 10 +++++-----
4 files changed, 7 insertions(+), 9 deletions(-)
diff --git a/Makefile b/Makefile
index a340d6a8..0f78c5ec 100644
--- a/Makefile
+++ b/Makefile
@@ -21,10 +21,8 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/closestBed \
$(SRC_DIR)/complementBed \
$(SRC_DIR)/coverageBed \
- $(SRC_DIR)/cuffToTrans \
$(SRC_DIR)/fastaFromBed \
$(SRC_DIR)/flankBed \
- $(SRC_DIR)/fjoin \
$(SRC_DIR)/genomeCoverageBed \
$(SRC_DIR)/intersectBed \
$(SRC_DIR)/linksBed \
diff --git a/src/pairToPair/pairToPair.cpp b/src/pairToPair/pairToPair.cpp
index 00daa46c..8cc90e77 100644
--- a/src/pairToPair/pairToPair.cpp
+++ b/src/pairToPair/pairToPair.cpp
@@ -124,7 +124,7 @@ void PairToPair::FindOverlaps(const BEDPE &a) {
if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0))
found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2);
- if (!found1 && !found2)
+ if (!found1 || !found2)
_bedA->reportBedPENewLine(a);
}
else if (_searchType == "either") {
diff --git a/src/pairToPair/pairToPair.h b/src/pairToPair/pairToPair.h
index d69c5724..77d739c2 100644
--- a/src/pairToPair/pairToPair.h
+++ b/src/pairToPair/pairToPair.h
@@ -65,7 +65,7 @@ private:
void FindQualityHitsBetweenEnds(CHRPOS start, CHRPOS end,
const vector<MATE> &hits, vector<MATE> &qualityHits, int &numOverlaps);
- void FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
+ bool FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
const vector<MATE> &qualityHitsEnd2);
void FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
diff --git a/src/pairToPair/pairToPairMain.cpp b/src/pairToPair/pairToPairMain.cpp
index 97115f68..7f5761d0 100644
--- a/src/pairToPair/pairToPairMain.cpp
+++ b/src/pairToPair/pairToPairMain.cpp
@@ -122,8 +122,8 @@ int main(int argc, char* argv[]) {
showHelp = true;
}
- if (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either")) {
- cerr << endl << "*****" << endl << "*****ERROR: Request \"both\" or \"neither\"" << endl << "*****" << endl;
+ if (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either") && (searchType != "notboth")) {
+ cerr << endl << "*****" << endl << "*****ERROR: Request \"both\",\"neither\",\"either\",or \"notboth\"" << endl << "*****" << endl;
showHelp = true;
}
@@ -160,11 +160,11 @@ void ShowHelp(void) {
cerr << "\t-type \t" << "Approach to reporting overlaps between A and B." << endl << endl;
cerr << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
-
cerr << "\t\teither\tReport overlaps if either ends of A overlap B." << endl;
-
cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
- cerr << "\t\t\t- Default = both." << endl << endl;
+ cerr << "\t\tnotboth\tReport overlaps if one or neither of ends of A overlap B." << endl;
+
+ cerr << "\t\t- Default = both." << endl << endl;
cerr << "\t-slop \t" << "The amount of slop (in b.p.). to be added to each footprint." << endl;
cerr << "\t\t*Note*: Slop is subtracted from start1 and start2 and added to end1 and end2." << endl << endl;
--
GitLab