Add btllib as a dependancy (#152)

* Removed packaged btllib, make a dependency

* Fix conda install command

* add parameter to conda install in CI

* Update Common/Makefile.am

* Update CI

* Fix yml formatting

* Activate conda env for all compile steps

* Fix for clang-tidy, ensure clang-tidy reads CXXFLAGS

* Update README

* Add mac to CI

* CI format fix

* CI format fix

* CI fix formatting

* Set unused-but-set-variable to be warning, not error

Arcs/Makefile.am

@@ -1,6 +1,6 @@
 bin_PROGRAMS = arcs
 
-arcs_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
+arcs_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS) -Wno-error=unused-but-set-variable
 
 arcs_CPPFLAGS = -I$(top_srcdir)/Arcs \
 	-I$(top_srcdir)/Common \

Common/Makefile.am

@@ -1,6 +1,6 @@
 noinst_LIBRARIES = libcommon.a
 
-libcommon_a_CPPFLAGS = -I$(top_srcdir)
+libcommon_a_CPPFLAGS = -I$(top_srcdir) -Wno-error=unused-result
 
 libcommon_a_SOURCES = \
 	BloomFilter.cpp BloomFilter.h \

README.md

@@ -18,11 +18,12 @@ Because ARKS is not dependent on read alignments, it is generally much faster th
 
 ### Dependencies
 * Boost (tested on 1.61)
-* GCC (5.1+)
+* GCC (6+)
 * Autotools (if cloning directly from repository) 
 * LINKS (tested on 1.8)
 * Google SparseHash
 * ABySS (if using long reads) (tested on 2.2.5)
+* [btllib](https://github.com/bcgsc/btllib) (1.4.3+)
 
 ### Compilation:
 If cloning directly from the repository run:
@@ -41,6 +42,12 @@ If your boost library headers are not in your PATH you can specify their locatio
 ```
 ./configure –-with-boost=/boost/path --prefix=/ARCS/PATH && make install
 ```
+If you compiled btllib from source (as opposed to installation using conda), you can specify the location of the btllib library files:
+```
+export CXXFLAGS+=" -I /path/to/btllib/include"
+export LDFLAGS+=" -L /path/to/btllib/install/lib"
+./configure && make
+```
 
 ### ARCS+LINKS Pipeline
 

azure-pipelines.yml

@@ -7,15 +7,14 @@ jobs:
   steps:
   - script: echo "##vso[task.prependpath]$CONDA/bin"
     displayName: Add conda to PATH
-
   - script: conda create --yes --quiet --name arcs_CI
     displayName: Create Anaconda environment
-
   - script: |
-      sudo apt-get update -qq
-      sudo apt-get install -qq libboost-dev libsparsehash-dev automake
-    displayName: Install C++ modules
+      source activate arcs_CI
+      conda install --yes -c conda-forge -c bioconda compilers btllib boost automake sparsehash
+    displayName: Install dependencies
   - script: |
+      source activate arcs_CI
       ./autogen.sh
       ./configure
       make
@@ -30,7 +29,9 @@ jobs:
       pylint makeTSVfile.py
       cd ../
     displayName: Run pylint
-  - script: make distcheck
+  - script: |
+      source activate arcs_CI
+      make distcheck
     displayName: Compile ARCS with make distcheck
   - script: |
       curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
@@ -39,8 +40,32 @@ jobs:
       sudo apt-get install -y --no-install-recommends clang-format clang-tidy
     displayName: Install clang-format and clang-tidy
   - script: |
+      source activate arcs_CI
       make -C Arcs clang-format
       make -C src lint
     displayName: Run clang-format
-  - script: make -C src all
+  - script: |
+      source activate arcs_CI
+      make -C src all
     displayName: Compile long-to-linked-pe
+
+- job:
+  displayName: mac-latest
+  pool:
+    vmImage: 'macOS-latest'
+
+  steps:
+  - script: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+  - script: conda create --yes --quiet --name arcs_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate arcs_CI
+      conda install --yes -c conda-forge -c bioconda compilers btllib boost automake sparsehash
+    displayName: Install dependencies
+  - script: |
+      source activate arcs_CI
+      ./autogen.sh
+      ./configure
+      make
+    displayName: Compile ARCS

src/Makefile.am

@@ -1,24 +1,19 @@
 bin_PROGRAMS = long-to-linked-pe
 
-long_to_linked_pe_CXXFLAGS = -O3 -Wall -Werror -Wno-unknown-pragmas -std=c++11 -pthread -I$(top_srcdir)/src/include
+long_to_linked_pe_CXXFLAGS = -O3 -Wall -Werror -Wno-unknown-pragmas -std=c++17 -pthread -I$(top_srcdir)/src/include 
 
-CXXFLAGS =  $(long_to_linked_pe_CXXFLAGS)
+CXXFLAGS += $(long_to_linked_pe_CXXFLAGS)
 
-long_to_linked_pe_SOURCES = long-to-linked-pe.cpp \
-	include/btllib/seq_reader.hpp \
-	include/btllib/status.hpp \
-	include/btllib/util.hpp \
-	include/btllib/cstring.hpp \
-	include/btllib/data_stream.hpp \
-	include/btllib/order_queue.hpp \
-	include/btllib/seq.hpp
+long_to_linked_pe_LDADD = -lbtllib
+
+long_to_linked_pe_SOURCES = long-to-linked-pe.cpp 
 
 # Check the C++ source code for errors.
 lint: clang-format clang-tidy
 
 # Check the C++ source code for errors with clang-tidy.
 clang-tidy:
-	clang-tidy -warnings-as-errors='*' *.cpp -- -std=c++11 -x c++ -Ibtllib/include -Iinclude
+	clang-tidy -warnings-as-errors='*' *.cpp -- -std=c++11 -x c++  ${CXXFLAGS}
 
 # Check the C++ source code for white-space errors with clang-format.
 clang-format: