From d71889baa42506f1fbe4016e193bc133f29b954f Mon Sep 17 00:00:00 2001
From: Robert A Petit III <robbie.petit@gmail.com>
Date: Mon, 29 Jun 2020 20:14:07 -0400
Subject: [PATCH] renamed VERSION to BOWTIE2_VERSION

---
 BOWTIE2_VERSION | 1 +
 CMakeLists.txt  | 2 +-
 Makefile        | 6 +++---
 VERSION         | 1 -
 doc/release.txt | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)
 create mode 100644 BOWTIE2_VERSION
 delete mode 100644 VERSION

diff --git a/BOWTIE2_VERSION b/BOWTIE2_VERSION
new file mode 100644
index 000000000..acdc3f1b0
--- /dev/null
+++ b/BOWTIE2_VERSION
@@ -0,0 +1 @@
+2.4.2
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 09870962a..aaaab73ff 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 2.8)
 cmake_policy(SET CMP0048 NEW)
 cmake_policy(SET CMP0005 NEW)
 
-file(STRINGS ${CMAKE_SOURCE_DIR}/VERSION PROJECT_VERSION)
+file(STRINGS ${CMAKE_SOURCE_DIR}/BOWTIE2_VERSION PROJECT_VERSION)
 project(bowtie2 LANGUAGES CXX VERSION ${PROJECT_VERSION})
 
 enable_testing()
diff --git a/Makefile b/Makefile
index 9b6a46e28..3375f6a09 100644
--- a/Makefile
+++ b/Makefile
@@ -187,7 +187,7 @@ BUILD_CPPS := diff_sample.cpp
 BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_build_main.cpp
 
 SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
-VERSION := $(shell cat VERSION)
+VERSION := $(shell cat BOWTIE2_VERSION)
 
 SANITIZER_FLAGS :=
 ifeq (0,$(shell $(CXX) -E -fsanitize=address,undefined btypes.h > /dev/null 2>&1; echo $$?))
@@ -282,7 +282,7 @@ GENERAL_LIST := $(wildcard scripts/*.sh) \
   MANUAL.markdown \
   README.md \
   TUTORIAL \
-  VERSION
+  BOWTIE2_VERSION
 
 ifeq (1,$(WINDOWS))
   BOWTIE2_BIN_LIST := $(BOWTIE2_BIN_LIST) bowtie2.bat bowtie2-build.bat bowtie2-inspect.bat
@@ -321,7 +321,7 @@ both-debug: bowtie2-align-s-debug bowtie2-build-s-debug bowtie2-align-l-debug bo
 both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-align-l-sanitized bowtie2-build-l-sanitized ;
 
 DEFS := -fno-strict-aliasing \
-  -DBOWTIE2_VERSION="\"`cat VERSION`\"" \
+  -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
   -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" \
   -DBUILD_TIME="\"`date -u`\"" \
   -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
diff --git a/VERSION b/VERSION
deleted file mode 100644
index 005119baa..000000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-2.4.1
diff --git a/doc/release.txt b/doc/release.txt
index b1dd59222..836b25004 100644
--- a/doc/release.txt
+++ b/doc/release.txt
@@ -27,7 +27,7 @@ Prerequisites:
     changed.
     - TODO!  Need infrastructure for this.
 
- 5. Update VERSION with new version number if this hasn't already been done.
+ 5. Update BOWTIE2_VERSION with new version number if this hasn't already been done.
 
  6. Update NEWS and doc/website/recent_news.ssi if this hasn't already been
     done. (And even if it has, make sure the release date mentioned in those