Use autotools instead of a makefile

.gitignore

@@ -45,3 +45,15 @@ zstd/
 # Binary and library
 tachyon
 lib*.so.*
+
+**.deps
+**.dirstamp
+/autom4te.cache/
+Makefile
+config.h
+configure.scan
+coverage_report
+stamp-h1
+autoscan.log
+config.log
+config.status

.travis.yml

@@ -3,14 +3,44 @@ language: cpp
 dist: trusty
 matrix:
   include:
+    # OSX begin
+    - os: osx
+      osx_image: xcode10
+      env:
+        - MATRIX_EVAL="brew update && brew install gcc@5 && brew install openssl && brew install pkg-config && CC=gcc-5 && CXX=g++-5"
+      script:
+        - sudo ntpdate -u time.apple.com
+
+    - os: osx
+      osx_image: xcode10
+      env:
+        - MATRIX_EVAL="brew update && brew install gcc@6 && brew install openssl && brew install pkg-config && CC=gcc-6 && CXX=g++-6"
+      script:
+        - sudo ntpdate -u time.apple.com
+
+    - os: osx
+      osx_image: xcode10
+      env:
+        - MATRIX_EVAL="brew update && brew install gcc@7 && brew install openssl && brew install pkg-config && CC=gcc-7 && CXX=g++-7"
+      script:
+        - sudo ntpdate -u time.apple.com
+
+    - os: osx
+      osx_image: xcode10
+      env:
+        - MATRIX_EVAL="brew update && brew install gcc@8 && brew install openssl && brew install pkg-config && CC=gcc-8 && CXX=g++-8"
+      script:
+        - sudo ntpdate -u time.apple.com
+
     # works on Precise and Trusty
     - os: linux
       addons:
         apt:
           sources:
             - ubuntu-toolchain-r-test
+            - llvm-toolchain-precise-3.7
           packages:
-            - g++-4.9
+            - clang-3.7
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -22,8 +52,8 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-         - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9"
-      compiler: gcc
+        - MATRIX_EVAL="CC=clang-3.7 && CXX=clang++-3.7"
+      compiler: clang
 
     # works on Precise and Trusty
     - os: linux
@@ -32,7 +62,7 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-5
+            - g++-4.9
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -44,7 +74,7 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-         - MATRIX_EVAL="CC=gcc-5 && CXX=g++-5"
+         - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9"
       compiler: gcc
 
     # works on Precise and Trusty
@@ -54,7 +84,7 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-6
+            - g++-5
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -66,7 +96,7 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-        - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
+         - MATRIX_EVAL="CC=gcc-5 && CXX=g++-5"
       compiler: gcc
 
     # works on Precise and Trusty
@@ -76,7 +106,7 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-7
+            - g++-6
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -88,7 +118,7 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+        - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
       compiler: gcc
 
     # works on Precise and Trusty
@@ -98,7 +128,7 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-8
+            - g++-7
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -110,7 +140,7 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-        - MATRIX_EVAL="CC=gcc-8 && CXX=g++-8"
+        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
       compiler: gcc
 
     # works on Precise and Trusty
@@ -119,9 +149,8 @@ matrix:
         apt:
           sources:
             - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.7
           packages:
-            - clang-3.7
+            - g++-8
             - pkg-config
             - libncurses5-dev
             - libncursesw5-dev
@@ -133,8 +162,8 @@ matrix:
             - libbz2-dev
             - liblzma-dev
       env:
-        - MATRIX_EVAL="CC=clang-3.7 && CXX=clang++-3.7"
-      compiler: clang
+        - MATRIX_EVAL="CC=gcc-8 && CXX=g++-8"
+      compiler: gcc
 
     # works on Precise and Trusty
     - os: linux
@@ -273,35 +302,17 @@ matrix:
         - MATRIX_EVAL="CC=clang-7 && CXX=clang++-7"
       compiler: clang
 
-    # OSX begin
-    - os: osx
-      osx_image: xcode10
-      env:
-        - MATRIX_EVAL="brew update && brew install gcc@5 && brew install openssl && CC=gcc-5 && CXX=g++-5
-
-    - os: osx
-      osx_image: xcode10
-      env:
-        - MATRIX_EVAL="brew update && brew install gcc@6 && brew install openssl && CC=gcc-6 && CXX=g++-6
-
-    - os: osx
-      osx_image: xcode10
-      env:
-        - MATRIX_EVAL="brew update && brew install gcc@7 && brew install openssl && CC=gcc-7 && CXX=g++-7
-
-    - os: osx
-      osx_image: xcode10
-      env:
-        - MATRIX_EVAL="brew update && brew install gcc@8 && brew install openssl && CC=gcc-8 && CXX=g++-8
 
 before_install:
   - eval "${MATRIX_EVAL}"
+  - git clone https://github.com/Cyan4973/xxHash
+  - cd xxHash && CFLAGS='-D__OPTIMIZE_SIZE__=1' make -j4 && sudo make install && cd ..
   - git clone https://github.com/facebook/zstd
   - cd zstd && make -j4 && sudo make install && cd ..
   - git clone https://github.com/samtools/htslib
   - cd htslib && autoheader && autoconf && ./configure && make -j 4 && sudo make install && cd ..
 
 script:
   - git submodule update --recursive
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make -j 4 OPENSSL_PATH=/usr/local/opt/openssl/; else make -j 4; fi
-
+  - ./configure && make -j 4
+

Makefile.am

@@ -0,0 +1,9 @@
+ACLOCAL_AMFLAGS = -I m4
+lib_LTLIBRARIES = libtachyon.la
+libtachyon_la_SOURCES = src/algorithm/compression/uncompressed_codec.cpp src/algorithm/compression/zstd_codec.cpp  src/algorithm/compression/genotype_encoder.cpp src/algorithm/compression/compression_manager.cpp src/algorithm/permutation/genotype_sorter.cpp src/algorithm/encryption/encryption.cpp src/algorithm/digest/variant_digest_manager.cpp  src/core/variant_record.cpp src/core/genotypes.cpp src/core/header_footer.cpp src/core/variant_reader_filters.cpp src/variant_reader.cpp src/containers/data_container.cpp src/containers/primitive_container.cpp src/containers/variant_container.cpp src/containers/interval_container.cpp src/containers/checksum_container.cpp src/containers/variant_block.cpp src/containers/vcf_container.cpp src/vcf_importer_slave.cpp src/support/utility.cpp src/support/support_vcf.cpp src/support/fisher_math.cpp src/support/tachyon.cpp src/io/buffer.cpp src/io/variant_writer.cpp src/io/basic_reader.cpp src/io/vcf_utils.cpp src/variant_importer.cpp src/index/index_record.cpp src/index/index.cpp src/index/variant_index_contig.cpp src/index/variant_index_quad_tree.cpp include/buffer.h            include/primitive_container.h     include/variant_record.h                           src/algorithm/digest/variant_digest_manager.h  src/containers/vcf_container.h           src/io/basic_reader.h include/config.h            include/support_vcf.h             include/variant_writer.h                           src/algorithm/parallel/variant_base_slave.h    src/core/variant_reader_filters_tuple.h  src/io/vcf_reader.h include/data_container.h    include/tachyon.h                 src/algorithm/compression/compression_container.h  src/algorithm/parallel/variant_slaves.h        src/import.h                             src/io/vcf_utils.h include/encryption.h        include/utility.h                 src/algorithm/compression/compression_manager.h    src/algorithm/parallel/vcf_slaves.h            src/index/variant_index_bin.h            src/program_utils.h include/generic_iterator.h  include/variant_block.h           src/algorithm/compression/genotype_encoder.h       src/algorithm/permutation/genotype_sorter.h    src/index/variant_index_contig.h         src/stats.h include/genotypes.h         include/variant_container.h       src/algorithm/compression/uncompressed_codec.h     src/algorithm/spinlock.h                       src/index/variant_index_linear.h         src/support/fisher_math.h include/header_footer.h     include/variant_importer.h        src/algorithm/compression/zstd_codec.h             src/algorithm/timer.h*                         src/index/variant_index_meta_entry.h     src/third_party/intervalTree.h include/index.h             include/variant_reader_filters.h  src/algorithm/digest/digest.h                      src/containers/checksum_container.h            src/index/variant_index_meta.h           src/vcf_importer_slave.h include/index_record.h      include/variant_reader.h          src/algorithm/digest/digest_manager.h              src/containers/interval_container.h            src/index/variant_index_quad_tree.h      src/view.h
+libtachyon_la_LDFLAGS = -shared
+bin_PROGRAMS = tachyon
+tachyon_SOURCES = src/main.cpp
+tachyon_CFLAGS = -pthread
+tachyon_CXXFLAGS = -pthread
+tachyon_LDADD = libtachyon.la