From 44dba68c4542b25635db5607df41ba2b4b5c0aee Mon Sep 17 00:00:00 2001
From: cwright <chris.wright@nanoporetech.com>
Date: Tue, 3 Apr 2018 15:39:25 +0100
Subject: [PATCH 1/2] Add bcftools

---
 Makefile | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 70e3ff0..2a8105c 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ OS := $(shell uname)
 CXX         ?= g++
 
 # Builds a cache of binaries which can just be copied for CI
-BINARIES=minimap2 miniasm bwa racon samtools
+BINARIES=minimap2 miniasm bwa racon samtools bcftools
 
 BINCACHEDIR=bincache
 $(BINCACHEDIR):
@@ -30,7 +30,6 @@ $(BINCACHEDIR)/racon: | $(BINCACHEDIR)
 	cd submodules/racon/build && make
 	cp submodules/racon/build/bin/racon $@
 
-
 $(BINCACHEDIR)/bwa: | $(BINCACHEDIR)
 	@echo Making $(@F)
 	cd submodules/bwa && make
@@ -49,6 +48,17 @@ $(BINCACHEDIR)/samtools: | $(BINCACHEDIR)
 	cd submodules/samtools-${SAMVER} && make
 	cp submodules/samtools-${SAMVER}/samtools $@
 
+BCFVER=1.7
+$(BINCACHEDIR)/bcftools: | $(BINCACHEDIR)
+	@echo Making $(@F)
+	if [ ! -e submodules/bcftools-${SAMVER}.tar.bz2 ]; then \
+	  cd submodules; \
+	  wget https://github.com/samtools/bcftools/releases/download/${BCFVER}/bcftools-${BCFVER}.tar.bz2; \
+	fi
+	cd submodules && tar -xjf bcftools-${BCFVER}.tar.bz2
+	cd submodules/bcftools-${BCFVER} && make
+	cp submodules/bcftools-${BCFVER}/bcftools $@
+
 venv: venv/bin/activate
 IN_VENV=. ./venv/bin/activate
 

From 9b817f03056813835d6a34455c7de0121f69ac46 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Thu, 12 Apr 2018 09:31:56 +0100
Subject: [PATCH 2/2] Update Makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 2a8105c..040fb87 100644
--- a/Makefile
+++ b/Makefile
@@ -51,7 +51,7 @@ $(BINCACHEDIR)/samtools: | $(BINCACHEDIR)
 BCFVER=1.7
 $(BINCACHEDIR)/bcftools: | $(BINCACHEDIR)
 	@echo Making $(@F)
-	if [ ! -e submodules/bcftools-${SAMVER}.tar.bz2 ]; then \
+	if [ ! -e submodules/bcftools-${BCFVER}.tar.bz2 ]; then \
 	  cd submodules; \
 	  wget https://github.com/samtools/bcftools/releases/download/${BCFVER}/bcftools-${BCFVER}.tar.bz2; \
 	fi