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Merge pull request #377 from DEploid-dev/shajoezhu-patch-1
Update config.yml
2 parents 704d178 + f757ec9 commit f637f98

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‎.circleci/config.yml‎

Lines changed: 55 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,11 @@
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version: 2.0
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version: 2.1
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orbs:
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coveralls: coveralls/coveralls@2.2.5
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jobs:
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"14.04":
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v1804:
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docker:
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- image: circleci/buildpack-deps:14.04
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- image: cimg/base:2022.08-18.04
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working_directory: /home/circleci/DEploid
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steps:
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- checkout
@@ -16,35 +19,35 @@ jobs:
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- run:
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name: Install dependencies and set path
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command: |
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev
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sudo apt-get install valgrind
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev
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sudo apt-get install valgrind
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- run:
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name: Getting ready
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command: |
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name: Getting ready
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command: |
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g++ --version
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./bootstrap
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- run:
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name: Compile
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command: |
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name: Compile
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command: |
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make
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sudo make install
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make check
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- run:
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name: Run tests
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command: |
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name: Run tests
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command: |
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./tests/test_binary.sh
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./tests/testPOS.sh
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./tests/test_binaryVcfVsTxt.sh
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./tests/test-against-previous-version.sh
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./tests/test_binaryReproducible.sh
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#- valgrind --leak-check=full -v --show-leak-kinds=all ./unit_tests
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#- coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
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#- coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
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"16.04":
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v2004:
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docker:
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- image: circleci/buildpack-deps:16.04
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- image: cimg/base:2022.08 # stable-20.04
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working_directory: /home/circleci/DEploid
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steps:
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- checkout
@@ -58,33 +61,33 @@ jobs:
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- run:
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name: Install dependencies and set path
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command: |
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev
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sudo apt-get install valgrind
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev
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sudo apt-get install valgrind
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- run:
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name: Getting ready
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command: |
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name: Getting ready
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command: |
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g++ --version
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./bootstrap
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- run:
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name: Compile
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command: |
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name: Compile
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command: |
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make
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sudo make install
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make check
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- run:
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name: Run tests
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command: |
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name: Run tests
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command: |
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./tests/test_binary.sh
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./tests/testPOS.sh
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./tests/test_binaryVcfVsTxt.sh
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./tests/test-against-previous-version.sh
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./tests/test_binaryReproducible.sh
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"20.04":
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v2204:
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docker:
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- image: circleci/buildpack-deps:20.04
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- image: cimg/base:2024.12
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working_directory: /home/circleci/DEploid
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steps:
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- checkout
@@ -98,35 +101,38 @@ jobs:
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- run:
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name: Install dependencies and set path
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command: |
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev
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sudo apt-get install valgrind
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sudo apt-get update
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curl -fsSL https://git.io/vHGMF | bash
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sudo apt-get install libcppunit-dev automake
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sudo apt-get install valgrind lcov
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- run:
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name: Getting ready
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command: |
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name: Getting ready
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command: |
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g++ --version
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./bootstrap
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- run:
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name: Compile
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command: |
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name: Compile
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command: |
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make
114117
sudo make install
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make check
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- run:
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name: Run tests
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command: |
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./tests/test_binary.sh
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./tests/testPOS.sh
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./tests/test_binaryVcfVsTxt.sh
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./tests/test-against-previous-version.sh
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./tests/test_binaryReproducible.sh
124-
120+
name: Run tests
121+
command: |
122+
# ./tests/test_binary.sh
123+
# ./tests/testPOS.sh
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# ./tests/test_binaryVcfVsTxt.sh
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# ./tests/test-against-previous-version.sh
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# ./tests/test_binaryReproducible.sh
127+
# valgrind --leak-check=full -v --show-leak-kinds=all ./unit_tests_1
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# coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
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./tests/test-coverage-coverall.sh
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- coveralls/upload
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126132
workflows:
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version: 2
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build:
133+
myworkflow:
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jobs:
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- "20.04"
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# - "14.04"
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# - "16.04"
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- v2204
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- v2004
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# - v1804 # this is too old, bash_complete not available
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‎Makefile.am‎

Lines changed: 25 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ bin_PROGRAMS = dEploid dEploid_dbg
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man1_MANS = docs/_build/man/dEploid.1
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1515
TESTS = unit_tests io_unit_tests
16-
check_PROGRAMS = unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
16+
check_PROGRAMS = unit_tests_1 unit_tests_2 unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
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PROG = DEPLOID
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1919
common_flags = -std=c++17 -Isrc/ -Isrc/codeCogs/ -Isrc/vcf/src/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall -Wextra
@@ -57,19 +57,37 @@ dEploid_LDADD = $(common_LDADD)
5757
dEploid_dbg_LDADD = $(common_LDADD)
5858
dEploid_prof_LDADD = $(common_LDADD)
5959

60-
unit_tests_SOURCES = $(common_src) \
61-
tests/unittest/test_runner.cpp \
62-
tests/unittest/test_ibd.cpp \
63-
tests/unittest/test_updateSingleHap.cpp \
64-
tests/unittest/test_utilities.cpp \
60+
unit_tests_1_SOURCES_0 = tests/unittest/test_ibd.cpp \
6561
tests/unittest/test_panel.cpp \
66-
tests/unittest/test_mcmc.cpp \
62+
tests/unittest/test_utilities.cpp
63+
64+
unit_tests_2_SOURCES_0 = tests/unittest/test_mcmc.cpp \
65+
tests/unittest/test_updateSingleHap.cpp \
6766
tests/unittest/test_updatePairHap.cpp \
6867
tests/unittest/test_workflow.cpp
6968

69+
unit_tests_1_SOURCES = $(common_src) \
70+
$(unit_tests_1_SOURCES_0) \
71+
tests/unittest/test_runner.cpp
72+
73+
unit_tests_2_SOURCES = $(common_src) \
74+
$(unit_tests_2_SOURCES_0) \
75+
tests/unittest/test_runner.cpp
76+
77+
unit_tests_SOURCES = $(common_src) \
78+
$(unit_tests_1_SOURCES_0) \
79+
$(unit_tests_2_SOURCES_0) \
80+
tests/unittest/test_runner.cpp
81+
7082
unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
7183
unit_tests_LDADD = -lcppunit -ldl $(common_LDADD)
7284

85+
unit_tests_1_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
86+
unit_tests_1_LDADD = -lcppunit -ldl $(common_LDADD)
87+
88+
unit_tests_2_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
89+
unit_tests_2_LDADD = -lcppunit -ldl $(common_LDADD)
90+
7391
io_unit_tests_SOURCES = $(common_src) \
7492
tests/unittest/test_runner.cpp \
7593
tests/unittest/test_dEploidIO.cpp

‎bootstrap‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,5 +23,5 @@ echo " done."
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2424
aclocal
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autoconf
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automake -a
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automake -a --force-missing --add-missing
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./configure

‎src/vcf‎

‎tests/test-coverage-coverall.sh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
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make -mj
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66
# Generate html report
7-
lcov --ignore-errors version --base-directory . --directory . --zerocounters -q
7+
lcov --base-directory . --directory . --zerocounters -q
88
make check -mj
9-
lcov --ignore-errors version --base-directory . --directory . -c -o coverage/lcov.info
9+
lcov --base-directory . --directory . -c -o coverage/lcov.info
1010
# --rc lcov_branch_coverage=1 option will turn on branch check
11-
lcov --ignore-errors version --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/vcf/*" "src/lasso/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries
11+
lcov --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/vcf/*" "src/lasso/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries

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