From d2070f8145e807a0d86816143fda3ea517caccb7 Mon Sep 17 00:00:00 2001
From: Joe Zhu <sha.joe.zhu@gmail.com>
Date: Tue, 9 Oct 2018 12:40:31 +0100
Subject: [PATCH] splitting unittests

---
 Makefile.am       | 18 ++++++++++++------
 src/dEploidIO.cpp |  3 +--
 src/dEploidIO.hpp |  1 +
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 1d3e4887..f25ad9e7 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -11,8 +11,8 @@ bin_PROGRAMS = dEploid dEploid_dbg utilities
 
 man1_MANS = docs/_build/man/dEploid.1
 
-TESTS = unit_tests
-check_PROGRAMS = unit_tests dEploid_dbg dEploid_prof
+TESTS = unit_tests io_unit_tests
+check_PROGRAMS = unit_tests dEploid_dbg dEploid_prof io_unit_tests
 PROG = DEPLOID
 
 common_flags = -std=c++0x -Isrc/ -Isrc/codeCogs/ -Isrc/random/ -Isrc/gzstream/ -Isrc/lasso/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\"
@@ -54,19 +54,25 @@ dEploid_prof_LDADD = $(common_LDADD)
 
 unit_tests_SOURCES = $(common_src) \
 					 tests/unittest/test_runner.cpp \
-					 tests/unittest/test_dEploidIO.cpp \
 					 tests/unittest/test_ibd.cpp \
 					 tests/unittest/test_updateSingleHap.cpp \
 					 tests/unittest/test_utilities.cpp \
 					 tests/unittest/test_panel.cpp \
-					 tests/unittest/test_txtReader.cpp \
 					 tests/unittest/test_mcmc.cpp \
-					 tests/unittest/test_updatePairHap.cpp \
-					 tests/unittest/test_vcfReader.cpp
+					 tests/unittest/test_updatePairHap.cpp
 
 unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
 unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)
 
+io_unit_tests_SOURCES = $(common_src) \
+					 tests/unittest/test_runner.cpp \
+					 tests/unittest/test_dEploidIO.cpp \
+					 tests/unittest/test_txtReader.cpp \
+					 tests/unittest/test_vcfReader.cpp
+
+io_unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
+io_unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)
+
 clean-local: clean-local-check
 .PHONY: clean-local-check utilities
 clean-local-check:
diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp
index a8edbe7a..23fe8ad0 100644
--- a/src/dEploidIO.cpp
+++ b/src/dEploidIO.cpp
@@ -822,8 +822,7 @@ void DEploidIO::dEploidLasso() {
         vector < vector <double> > tmpPanel = lassoSubsetPanel(start, length);
         DEploidLASSO dummy(tmpPanel, wsaf, 250);
         lassoPanels.push_back(dummy.reducedPanel);
-
-
+        lassoPlafs.push_back(vector <double> (plaf_.begin()+start, plaf_.begin()+start+length));
 
         // for (size_t i = 0; i < dummy.choiceIdx.size(); i++) {
             // cout << dummy.choiceIdx[i] << " " ;
diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp
index 47a752b3..7986e337 100644
--- a/src/dEploidIO.hpp
+++ b/src/dEploidIO.hpp
@@ -174,6 +174,7 @@ class DEploidIO{
 
     // Lasso Related
     vector < vector < vector <double> > > lassoPanels;
+    vector < vector <double> > lassoPlafs;
 
     // Parameters
     double missCopyProb_;