From 0ef7f2dd056c7bb899e04b1610c9162bf1fb39eb Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 8 Dec 2011 16:05:24 -0500
Subject: [PATCH] preliminary
---
Makefile | 6 +++++-
src/intersectBed/intersectMain.cpp | 10 +++++-----
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/Makefile b/Makefile
index 7a443d7f..35fa6bb6 100644
--- a/Makefile
+++ b/Makefile
@@ -9,6 +9,7 @@ SHELL := /bin/bash -e
export OBJ_DIR = obj
export BIN_DIR = bin
export SRC_DIR = src
+export UTIL_DIR = src/utils
export CXX = g++
export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
export LIBS = -lz
@@ -59,6 +60,8 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \
$(SRC_DIR)/utils/Fasta \
$(SRC_DIR)/utils/genomeFile
+BUILT_OBJECTS = $(OBJ_DIR)/*.o
+
all:
[ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
@@ -78,7 +81,8 @@ all:
echo ""; \
done
- echo "- Building main bedtools binary."
+ @echo "- Building main bedtools binary."
+ @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
.PHONY: all
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 3ae296de..f1af974a 100644
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -22,9 +22,9 @@ using namespace std;
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
// function declarations
-void ShowHelp(void);
+void intersect_help(void);
-int main(int argc, char* argv[]) {
+int intersect_main(int argc, char* argv[]) {
// our configuration variables
bool showHelp = false;
@@ -68,7 +68,7 @@ int main(int argc, char* argv[]) {
}
}
- if(showHelp) ShowHelp();
+ if(showHelp) intersect_help();
// do some parsing (all of these parameters require 2 strings)
for(int i = 1; i < argc; i++) {
@@ -223,11 +223,11 @@ int main(int argc, char* argv[]) {
return 0;
}
else {
- ShowHelp();
+ intersect_help();
}
}
-void ShowHelp(void) {
+void intersect_help(void) {
cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
--
GitLab