From 947e5dc18f997092ebc1b738b6adeff045bce24b Mon Sep 17 00:00:00 2001
From: martinghunt <martin.g.hunt@gmail.com>
Date: Mon, 14 Aug 2017 09:15:35 +0000
Subject: [PATCH 1/2] Change mapping options bor bowtie 2.3.1 and later

---
 ariba/mapping.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ariba/mapping.py b/ariba/mapping.py
index 718c2f5a..40564bae 100644
--- a/ariba/mapping.py
+++ b/ariba/mapping.py
@@ -1,5 +1,6 @@
 import os
 import sys
+from distutils.version import LooseVersion
 import pysam
 import pyfastaq
 from ariba import common
@@ -82,7 +83,7 @@ def run_bowtie2(
         '-2', reads_rev,
     ]
 
-    if bowtie2_version == '2.3.1':
+    if LooseVersion(bowtie2_version) >= LooseVersion('2.3.1'):
         map_cmd.append('--score-min G,1,10')
 
     if remove_both_unmapped:

From 20fe8c1fa49bc3fae7cf523e5ce778540cb9fba1 Mon Sep 17 00:00:00 2001
From: martinghunt <martin.g.hunt@gmail.com>
Date: Mon, 14 Aug 2017 09:16:50 +0000
Subject: [PATCH 2/2] Version bump 2.10.1

---
 Dockerfile | 2 +-
 setup.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 2bf55f83..c624a954 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,7 +28,7 @@ ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="a
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.10.0 \
+  && git checkout v2.10.1 \
   && python3 setup.py test \
   && python3 setup.py install
 
diff --git a/setup.py b/setup.py
index eda17e3a..b85411ee 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.10.0',
+    version='2.10.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},