Merge pull request #129 from mcveanlab/issue95

Issue95

.travis.yml

@@ -16,10 +16,12 @@ before_script:
 
 script:
   - make
+  - gzip -d data/testData/PG0390-C.test.vcf.gz
   - make check
   - ./tests/test_binary.sh
   - ./tests/testPOS.sh
   - ./tests/test_binaryVcfVsTxt.sh
+  - ./tests/test-against-previous-version.sh
 
 after_success:
   - coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'

Doxyfile

@@ -758,7 +758,8 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src/atMarker.hpp src/atMarker.cpp \
+INPUT                  = src/variantIndex.hpp src/variantIndex.cpp \
+                         src/txtReader.hpp src/txtReader.cpp \
                          src/mcmc.hpp src/mcmc.cpp   \
                          src/panel.hpp src/panel.cpp \
                          src/dEploid.cpp src/exceptions.hpp \

Makefile.am

@@ -25,7 +25,8 @@ common_src = src/random/fastfunc.cpp \
 			 src/dEploidIO.cpp \
 			 src/utility.cpp \
 			 src/updateHap.cpp \
-			 src/atMarker.cpp \
+			 src/txtReader.cpp \
+			 src/variantIndex.cpp \
 			 src/export/dEploidIOExport.cpp \
 			 src/export/dEploidIOExportPosteriorProb.cpp \
 			 src/vcfReader.cpp
@@ -42,15 +43,14 @@ dEploid_prof_CXXFLAGS = $(common_flags) -DNDEBUG -fno-omit-frame-pointer -pg -O1
 
 
 unit_tests_SOURCES = $(common_src) \
+					 tests/unittest/test_runner.cpp \
 					 tests/unittest/test_panel.cpp \
+					 tests/unittest/test_txtReader.cpp \
 					 tests/unittest/test_dEploidIO.cpp \
-					 tests/unittest/test_runner.cpp \
 					 tests/unittest/test_updatePairHap.cpp \
 					 tests/unittest/test_updateSingleHap.cpp \
-					 tests/unittest/test_atMarker.cpp \
 					 tests/unittest/test_utilities.cpp \
 					 tests/unittest/test_mcmc.cpp \
-					 tests/unittest/test_atMarker.cpp \
 					 tests/unittest/test_vcfReader.cpp
 
 unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage

circle.yml

@@ -16,9 +16,11 @@ test:
   override:
     - ./bootstrap
     - make
+    - gzip -d data/testData/PG0390-C.test.vcf.gz
     - make check
     #- valgrind  --leak-check=full -v --show-leak-kinds=all ./unit_tests
     - ./tests/test_binary.sh
     - ./tests/testPOS.sh
     - ./tests/test_binaryVcfVsTxt.sh
+    - ./tests/test-against-previous-version.sh
     #- coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'

data/exampleData/.gitignore

@@ -0,0 +1,3 @@
+labStrains.wg.PLAF.txt
+labStrains.wg.panel.txt
+labStrains_samples.vcf