Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Allow custom ploidy regions in HaplotypeCaller #8464

Closed
wants to merge 8 commits into from

Remove old commented code; add test arg copy sync deeper fields

3c18816
Select commit
Loading
Failed to load commit list.
Closed

Allow custom ploidy regions in HaplotypeCaller #8464

Remove old commented code; add test arg copy sync deeper fields
3c18816
Select commit
Loading
Failed to load commit list.
Codecov / codecov/patch succeeded Dec 8, 2023 in 1s

54.450% of diff hit (target 86.344%)

View this Pull Request on Codecov

54.450% of diff hit (target 86.344%)

Annotations

Check warning on line 27 in src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java#L27

Added line #L27 was not covered by tests

Check warning on line 34 in src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java#L29-L34

Added lines #L29 - L34 were not covered by tests

Check warning on line 93 in src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/MinimalGenotypingEngine.java#L93

Added line #L93 was not covered by tests

Check warning on line 214 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L213-L214

Added lines #L213 - L214 were not covered by tests

Check warning on line 219 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L219

Added line #L219 was not covered by tests

Check warning on line 221 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L221

Added line #L221 was not covered by tests

Check warning on line 647 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L647

Added line #L647 was not covered by tests

Check warning on line 685 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L685

Added line #L685 was not covered by tests

Check warning on line 867 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java#L867

Added line #L867 was not covered by tests

Check warning on line 209 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java#L209

Added line #L209 was not covered by tests

Check warning on line 463 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java#L463

Added line #L463 was not covered by tests

Check warning on line 483 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java#L483

Added line #L483 was not covered by tests

Check warning on line 524 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java#L524

Added line #L524 was not covered by tests

Check warning on line 547 in src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java#L547

Added line #L547 was not covered by tests

Check warning on line 952 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L952

Added line #L952 was not covered by tests

Check warning on line 956 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L954-L956

Added lines #L954 - L956 were not covered by tests

Check warning on line 958 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L958

Added line #L958 was not covered by tests

Check warning on line 962 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L962

Added line #L962 was not covered by tests

Check warning on line 964 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L964

Added line #L964 was not covered by tests

Check warning on line 968 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L968

Added line #L968 was not covered by tests

Check warning on line 971 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L970-L971

Added lines #L970 - L971 were not covered by tests

Check warning on line 976 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L976

Added line #L976 was not covered by tests

Check warning on line 980 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L978-L980

Added lines #L978 - L980 were not covered by tests

Check warning on line 982 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L982

Added line #L982 was not covered by tests

Check warning on line 986 in src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

See this annotation in the file changed.

@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java#L986

Added line #L986 was not covered by tests