From 67d15cc85fa4a6c2c38670901b91290eacd7e42e Mon Sep 17 00:00:00 2001
From: Chris Tomkins-Tinch <tomkinsc@gmail.com>
Date: Fri, 27 Jul 2018 17:14:18 -0400
Subject: [PATCH] bump pysam, samtools (#870)

samtools (and htslib) 1.7 -> 1.9
pysam 0.14.1 -> 0.15.0
---
 requirements-conda.txt | 4 ++--
 tools/samtools.py      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements-conda.txt b/requirements-conda.txt
index 2be002d0c..cb028bdce 100644
--- a/requirements-conda.txt
+++ b/requirements-conda.txt
@@ -21,7 +21,7 @@ parallel=20160622
 picard=2.18.11
 pigz=2.4
 prinseq=0.20.4
-samtools=1.7
+samtools=1.9
 snpeff=4.3.1t
 spades=3.11.1
 tbl2asn=25.6
@@ -35,6 +35,6 @@ bedtools=2.27.1
 biopython=1.72
 future==0.16.0
 matplotlib=1.5.3
-pysam=0.14.1
+pysam=0.15.0
 pybedtools=0.7.10
 PyYAML=3.12
diff --git a/tools/samtools.py b/tools/samtools.py
index 094a26d81..7d73aa7ac 100644
--- a/tools/samtools.py
+++ b/tools/samtools.py
@@ -33,7 +33,7 @@
 import util.misc
 
 TOOL_NAME = 'samtools'
-TOOL_VERSION = '1.7'
+TOOL_VERSION = '1.9'
 
 log = logging.getLogger(__name__)