Cleaned up bedFile.h and added -m64 to Makefiles

361bf23b · Aaron · ca0b7e3b · 361bf23b · 361bf23b · 361bf23b
Commit 361bf23b authored 15 years ago by Aaron
--- a/Makefile
+++ b/Makefile
@@ -8,20 +8,10 @@ export OBJ_DIR = obj
 export BIN_DIR = bin
 export SRC_DIR = src

-# define some default flags
-export CFLAGS ?= -Wall -O3
-export CXXFLAGS ?= $(CFLAGS)
-export LDFLAGS ?= -Wl,-s
-export CXX ?= g++
-
-# define our platform
-#export BLD_PLATFORM ?= linux64-core2
-#include includes/$(BLD_PLATFORM).inc
-
 # define our source subdirectories
 SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/bamToBed

-UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities
+UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools

 all:


--- a/bin/bamToBed
+++ b/bin/bamToBed
--- a/bin/closestBed
+++ b/bin/closestBed
--- a/bin/complementBed
+++ b/bin/complementBed
--- a/bin/coverageBed
+++ b/bin/coverageBed
--- a/bin/fastaFromBed
+++ b/bin/fastaFromBed
--- a/bin/genomeCoverageBed
+++ b/bin/genomeCoverageBed
--- a/bin/intersectBed
+++ b/bin/intersectBed
--- a/bin/linksBed
+++ b/bin/linksBed
--- a/bin/maskFastaFromBed
+++ b/bin/maskFastaFromBed
--- a/bin/mergeBed
+++ b/bin/mergeBed
--- a/bin/pairToBed
+++ b/bin/pairToBed
--- a/bin/pairToPair
+++ b/bin/pairToPair
--- a/bin/shuffleBed
+++ b/bin/shuffleBed
--- a/bin/slopBed
+++ b/bin/slopBed
--- a/bin/sortBed
+++ b/bin/sortBed
--- a/bin/subtractBed
+++ b/bin/subtractBed
--- a/bin/windowBed
+++ b/bin/windowBed
--- a/obj/bamToBed.o
+++ b/obj/bamToBed.o
--- a/obj/bedFile.o
+++ b/obj/bedFile.o