sci-biology/bedtools: [QA] Move patch to a distfile

Closes: https://bugs.gentoo.org/620612

3 files changed, 6 insertions, 873 deletions

diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index e398b3bee6f0..642fe852658e 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1 +1,2 @@
-DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2
+DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
+DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index eeedf606debe..0520143f3d9a 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -9,7 +9,8 @@ inherit flag-o-matic python-any-r1 toolchain-funcs
 
 DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
 HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -26,7 +27,7 @@ RDEPEND="sys-libs/zlib"
 S="${WORKDIR}/${PN}2"
 
 DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
+PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
 
 src_configure() {
 	append-lfs-flags
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
deleted file mode 100644
index fb6be18d7071..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,869 +0,0 @@
-* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308)
-* Remove CXX and CXXFLAGS, ebuild sets them
-* Handle python via Gentoo's EPYTHON instead
-
---- a/Makefile
-+++ b/Makefile
-@@ -16,17 +16,9 @@
- export BIN_DIR	= bin
- export SRC_DIR	= src
- export UTIL_DIR	= src/utils
--export CXX		= g++
--ifeq ($(DEBUG),1)
--export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
--else
--export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
--endif
- export LIBS		= -lz
- export BT_ROOT  = src/utils/BamTools/
- 
--prefix ?= /usr/local
--
- SUBDIRS = $(SRC_DIR)/annotateBed \
- 		  $(SRC_DIR)/bamToBed \
- 		  $(SRC_DIR)/bamToFastq \
-@@ -135,13 +127,13 @@
- 
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
- 	@echo "- Building main bedtools binary."
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
- 	@echo "done."
- 
- 	@echo "- Creating executables for old CLI."
--	@python scripts/makeBashScripts.py
--	@chmod +x bin/*
-+	$(EPYTHON) scripts/makeBashScripts.py
-+	chmod +x bin/*
- 	@echo "done."
- 
- 
---- a/src/annotateBed/Makefile
-+++ b/src/annotateBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 		
- clean:
---- a/src/bamToBed/Makefile
-+++ b/src/bamToBed/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)  -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bamToFastq/Makefile
-+++ b/src/bamToFastq/Makefile
-@@ -24,7 +24,7 @@
- 

- $(BUILT_OBJECTS): $(SOURCES)

- 	@echo "  * compiling" $(*F).cpp

--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 

-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp

- 

- clean:

- 	@echo "Cleaning up."

---- a/src/bed12ToBed6/Makefile
-+++ b/src/bed12ToBed6/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bedpeToBam/Makefile
-+++ b/src/bedpeToBam/Makefile
-@@ -33,7 +33,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
---- a/src/bedToBam/Makefile
-+++ b/src/bedToBam/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bedToIgv/Makefile
-+++ b/src/bedToIgv/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/closestFile/Makefile
-+++ b/src/closestFile/Makefile
-@@ -40,7 +40,7 @@
- 

- $(BUILT_OBJECTS): $(SOURCES)

- 	@echo "  * compiling" $(*F).cpp

--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)

-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp

- 

- clean:

- 	@echo "Cleaning up."

---- a/src/clusterBed/Makefile
-+++ b/src/clusterBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/complementFile/Makefile
-+++ b/src/complementFile/Makefile
-@@ -42,7 +42,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/coverageFile/Makefile
-+++ b/src/coverageFile/Makefile
-@@ -38,7 +38,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/expand/Makefile
-+++ b/src/expand/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/fastaFromBed/Makefile
-+++ b/src/fastaFromBed/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/fisher/Makefile
-+++ b/src/fisher/Makefile
-@@ -51,7 +51,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/flankBed/Makefile
-+++ b/src/flankBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 		
- clean:
- 	@echo "Cleaning up."
---- a/src/genomeCoverageBed/Makefile
-+++ b/src/genomeCoverageBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/getOverlap/Makefile
-+++ b/src/getOverlap/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 	
- clean:
---- a/src/groupBy/Makefile
-+++ b/src/groupBy/Makefile
-@@ -42,7 +42,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/intersectFile/Makefile
-+++ b/src/intersectFile/Makefile
-@@ -39,7 +39,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/jaccard/Makefile
-+++ b/src/jaccard/Makefile
-@@ -43,7 +43,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/linksBed/Makefile
-+++ b/src/linksBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/mapFile/Makefile
-+++ b/src/mapFile/Makefile
-@@ -38,7 +38,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/maskFastaFromBed/Makefile
-+++ b/src/maskFastaFromBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/mergeFile/Makefile
-+++ b/src/mergeFile/Makefile
-@@ -40,7 +40,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/multiBamCov/Makefile
-+++ b/src/multiBamCov/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/multiIntersectBed/Makefile
-+++ b/src/multiIntersectBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/nekSandbox1/Makefile
-+++ b/src/nekSandbox1/Makefile
-@@ -35,7 +35,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/nucBed/Makefile
-+++ b/src/nucBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/pairToBed/Makefile
-+++ b/src/pairToBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/pairToPair/Makefile
-+++ b/src/pairToPair/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 
- clean:
---- a/src/randomBed/Makefile
-+++ b/src/randomBed/Makefile
-@@ -23,7 +23,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/regressTest/Makefile
-+++ b/src/regressTest/Makefile
-@@ -24,24 +24,18 @@
- # ----------------------------------
- # define our source and object files
- # ----------------------------------
--#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
--#OBJECTS= regressTestMain.o RegressTest.o
--#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-+SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
-+OBJECTS= regressTestMain.o RegressTest.o
-+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
- PROGRAM= regressTest
- 
--
--all: #$(BUILT_OBJECTS)
--	@echo "compiling RegressTest.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
--	@echo "compiling regressTestMain.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+all: $(BUILT_OBJECTS)
- 	
- .PHONY: all
- 
--#$(BUILT_OBJECTS): $(SOURCES)
--#	@echo "  * compiling" $(*F).cpp
--#	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
--
-+$(BUILT_OBJECTS): $(SOURCES)
-+	@echo "  * compiling" $(*F).cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/reldist/Makefile
-+++ b/src/reldist/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/sampleFile/Makefile
-+++ b/src/sampleFile/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/shiftBed/Makefile
-+++ b/src/shiftBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/shuffleBed/Makefile
-+++ b/src/shuffleBed/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/slopBed/Makefile
-+++ b/src/slopBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/sortBed/Makefile
-+++ b/src/sortBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/spacingFile/Makefile
-+++ b/src/spacingFile/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/split/Makefile
-+++ b/src/split/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/subtractFile/Makefile
-+++ b/src/subtractFile/Makefile
-@@ -40,7 +40,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/tagBam/Makefile
-+++ b/src/tagBam/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/unionBedGraphs/Makefile
-+++ b/src/unionBedGraphs/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/BamTools/Makefile
-+++ b/src/utils/BamTools/Makefile
-@@ -56,12 +56,12 @@
- 
- $(LIBRARY): $(OBJECTS)
- 	@echo " * linking $(LIBRARY)"
--	ar cr $@ $^
-+	$(AR) cr $@ $^
- 	-ranlib $@
- 
- $(OBJECTS): $(SOURCES)
- 	@echo " * compiling" $(*F).cpp
--	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp
- 
- .PHONY: api
- api:
---- a/src/utils/BamTools-Ancillary/Makefile
-+++ b/src/utils/BamTools-Ancillary/Makefile
-@@ -21,7 +21,7 @@
- 

- $(BUILT_OBJECTS): $(SOURCES)

- 	@echo "  * compiling" $(*F).cpp

--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib

-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp

- 

- clean:

- 	@echo "Cleaning up."

---- a/src/utils/bedFile/Makefile
-+++ b/src/utils/bedFile/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/bedFilePE/Makefile
-+++ b/src/utils/bedFilePE/Makefile
-@@ -17,7 +17,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/bedGraphFile/Makefile
-+++ b/src/utils/bedGraphFile/Makefile
-@@ -19,7 +19,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/BinTree/Makefile
-+++ b/src/utils/BinTree/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/BlockedIntervals/Makefile
-+++ b/src/utils/BlockedIntervals/Makefile
-@@ -23,7 +23,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/chromsweep/Makefile
-+++ b/src/utils/chromsweep/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/Contexts/Makefile
-+++ b/src/utils/Contexts/Makefile
-@@ -36,7 +36,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/driver/Makefile
-+++ b/src/utils/driver/Makefile
-@@ -85,7 +85,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/Fasta/Makefile
-+++ b/src/utils/Fasta/Makefile
-@@ -19,7 +19,7 @@
- 	
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile
-@@ -32,7 +32,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile~
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile~
-@@ -31,7 +31,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/Makefile
-+++ b/src/utils/FileRecordTools/Makefile
-@@ -34,9 +34,9 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling FileRecordMgr.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp
- 	@echo "  * compiling FileRecordMergeMgr.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp
- 	
- 	
- 
---- a/src/utils/FileRecordTools/Records/Makefile
-+++ b/src/utils/FileRecordTools/Records/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/fileType/Makefile
-+++ b/src/utils/fileType/Makefile
-@@ -22,7 +22,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/general/Makefile
-+++ b/src/utils/general/Makefile
-@@ -21,7 +21,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/GenomeFile/Makefile
-+++ b/src/utils/GenomeFile/Makefile
-@@ -20,9 +20,9 @@
- 
- $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
- 	@echo "  * compiling GenomeFile.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp
- 	@echo "  * compiling NewGenomeFile.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp
- 
- #$(EXT_OBJECTS):
- #	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
---- a/src/utils/gzstream/Makefile
-+++ b/src/utils/gzstream/Makefile
-@@ -38,7 +38,7 @@
- UTILITIES_DIR = ../../utils/
- 	
- ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
--	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/KeyListOps/Makefile
-+++ b/src/utils/KeyListOps/Makefile
-@@ -31,7 +31,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 
- $(EXT_OBJECTS):
---- a/src/utils/NewChromsweep/Makefile
-+++ b/src/utils/NewChromsweep/Makefile
-@@ -34,7 +34,7 @@
- 

- $(BUILT_OBJECTS): $(SOURCES)

- 	@echo "  * compiling" $(*F).cpp

--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)

-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp

- 

- clean:

- 	@echo "Cleaning up."

---- a/src/utils/RecordOutputMgr/Makefile
-+++ b/src/utils/RecordOutputMgr/Makefile
-@@ -29,7 +29,7 @@
- 

- $(BUILT_OBJECTS): $(SOURCES)

- 	@echo "  * compiling" $(*F).cpp

--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)

-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp

- 

- $(EXT_OBJECTS):

- 	@$(MAKE) --no-print-directory -C $(INCLUDES)

---- a/src/utils/sequenceUtilities/Makefile
-+++ b/src/utils/sequenceUtilities/Makefile
-@@ -17,7 +17,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/tabFile/Makefile
-+++ b/src/utils/tabFile/Makefile
-@@ -19,7 +19,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/ToolBase/Makefile
-+++ b/src/utils/ToolBase/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/VectorOps/Makefile
-+++ b/src/utils/VectorOps/Makefile
-@@ -11,7 +11,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/version/Makefile
-+++ b/src/utils/version/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES) $(HEADERS)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/windowBed/Makefile
-+++ b/src/windowBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/windowMaker/Makefile
-+++ b/src/windowMaker/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/