Merge pull request #224 from tcezard/valid_missing_data

EVA-3338 - Missing data is valid even if multiple values are expected
EBIvariation · Jul 18, 2023 · 6807ed3 · 6807ed3
2 parents 3e1bd9b + 72f786c
commit 6807ed3
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Showing 5 changed files with 54 additions and 47 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -14,7 +14,7 @@ jobs:
 
   ### Linux build
   linux_build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         config:
@@ -60,57 +60,57 @@ jobs:
 
 
   ### Mac OS build
-  macos_build:
-    runs-on: macos-10.15
-    strategy:
-      matrix:
-        config:
-          - {cc: "gcc", cxx: "g++"}
-          - {cc: "clang", cxx: "clang++"}
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install dependencies
-      run: |
-        brew update
-        brew install boost sqlite3
-        ./install_dependencies.sh osx
-    - name: Compile and test
-      run: |
-        mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} ..
-        export LIBRARY_PATH=${LIBRARY_PATH}:/usr/local/opt/icu4c/lib
-        make -j2
-        cd .. && ./build/bin/test_validation_suite
-    - name: Rename release files
-      if: ${{ matrix.config.cc == 'clang' }}
-      run: |
-        mv build/bin/vcf_validator vcf_validator_macos
-        mv build/bin/vcf_debugulator vcf_debugulator_macos
-        mv build/bin/vcf_assembly_checker vcf_assembly_checker_macos
-    - name: Upload vcf-validator
-      uses: actions/upload-artifact@v3
-      if: ${{ matrix.config.cc == 'clang' }}
-      with:
-        name: vcf_validator_macos
-        path: vcf_validator_macos
-    - name: Upload vcf-debugulator
-      uses: actions/upload-artifact@v3
-      if: ${{ matrix.config.cc == 'clang' }}
-      with:
-        name: vcf_debugulator_macos
-        path: vcf_debugulator_macos
-    - name: Upload vcf-assembly-checker
-      uses: actions/upload-artifact@v3
-      if: ${{ matrix.config.cc == 'clang' }}
-      with:
-        name: vcf_assembly_checker_macos
-        path: vcf_assembly_checker_macos
+#  macos_build:
+#    runs-on: macos-11
+#    strategy:
+#      matrix:
+#        config:
+#          - {cc: "gcc", cxx: "g++"}
+#          - {cc: "clang", cxx: "clang++"}
+#
+#    steps:
+#    - uses: actions/checkout@v2
+#    - name: Install dependencies
+#      run: |
+#        brew update
+#        brew install boost sqlite3
+#        ./install_dependencies.sh osx
+#    - name: Compile and test
+#      run: |
+#        mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} ..
+#        export LIBRARY_PATH=${LIBRARY_PATH}:/usr/local/opt/icu4c/lib
+#        make -j2
+#        cd .. && ./build/bin/test_validation_suite
+#    - name: Rename release files
+#      if: ${{ matrix.config.cc == 'clang' }}
+#      run: |
+#        mv build/bin/vcf_validator vcf_validator_macos
+#        mv build/bin/vcf_debugulator vcf_debugulator_macos
+#        mv build/bin/vcf_assembly_checker vcf_assembly_checker_macos
+#    - name: Upload vcf-validator
+#      uses: actions/upload-artifact@v3
+#      if: ${{ matrix.config.cc == 'clang' }}
+#      with:
+#        name: vcf_validator_macos
+#        path: vcf_validator_macos
+#    - name: Upload vcf-debugulator
+#      uses: actions/upload-artifact@v3
+#      if: ${{ matrix.config.cc == 'clang' }}
+#      with:
+#        name: vcf_debugulator_macos
+#        path: vcf_debugulator_macos
+#    - name: Upload vcf-assembly-checker
+#      uses: actions/upload-artifact@v3
+#      if: ${{ matrix.config.cc == 'clang' }}
+#      with:
+#        name: vcf_assembly_checker_macos
+#        path: vcf_assembly_checker_macos
 
 
   ### Release job (tags only)
   create_release:
     if: startsWith(github.ref, 'refs/tags/')
-    needs: [ linux_build, macos_build ]
+    needs: [ linux_build ]
     runs-on: ubuntu-latest
     steps:
       - name: Download artifacts

diff --git a/src/vcf/record.cpp b/src/vcf/record.cpp
@@ -698,6 +698,9 @@ namespace ebi
             raise(std::make_shared<Error>(line, " meta specification Number=" + number
                     + " is not one of [A, R, G, ., <non-negative number>]"));
         }
+        if(!values.empty()) {
+            if (values.front() == MISSING_VALUE) { return; } // No need to check missing data
+        }
 
         bool number_matches = true;
         if (expected_cardinality > 0) {

diff --git a/test/input_files/v4.1/passed/passed_body_samples.vcf b/test/input_files/v4.1/passed/passed_body_samples.vcf
@@ -9,3 +9,4 @@
 1	300	rs180734498	C	T	100	PASS	AC=4	GT:MY	1/0:A	0|1:A,B,C
 1	400	rs180734498	C	T,A	100	PASS	AC=4,6	GT:CU	1/2:1,5	0|1:2,0
 1	500	rs180734498	C	T	100	PASS	AC=4	DP	1	4
+1	700	rs180734498	C	T	100	PASS	AC=4	GT:GL	0|0:.,.,.	0|1:.
diff --git a/test/input_files/v4.2/passed/passed_body_samples.vcf b/test/input_files/v4.2/passed/passed_body_samples.vcf
@@ -11,3 +11,4 @@
 1	400	rs180734498	C	T,A	100	PASS	AC=4,5	GT:CU	1/2:1,5	0|1:2,0
 1	500	rs180734498	C	T,G	100	PASS	AC=4,6	GT:CU2	1/2:-0.13,-0.58,-3.62	0|1:-2.45,-0.00,-5.00
 1	600	rs180734498	C	T	100	PASS	AC=4	DP	1	4
+1	700	rs180734498	C	T	100	PASS	AC=4	GT:GL	0|0:.,.,.	0|1:.
diff --git a/test/input_files/v4.3/passed/passed_body_samples.vcf b/test/input_files/v4.3/passed/passed_body_samples.vcf
@@ -11,3 +11,5 @@
 1	400	rs180734498	C	T,A	100	PASS	AC=4,5	GT:CU	1/2:1,5	0|1:2,0
 1	500	rs180734498	C	T,G	100	PASS	AC=4,6	GT:CU2	1/2:-0.13,-0.58,-3.62	0|1:-2.45,-0.00,-5.00
 1	600	rs180734498	C	T	100	PASS	AC=4	DP	1	4
+1	700	rs180734498	C	T	100	PASS	AC=4	GT:GL	0|0:.,.,.	0|1:.
+