Poc/methylation #143
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Poc/methylation #143
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dennishendriksen
commented
Feb 8, 2024
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The build failed with a Critical, Major and Minor code issue: https://sonarcloud.io/project/issues?id=molgenis_vip-report&pullRequest=143&resolved=false&inNewCodePeriod=true as well as test coverage being too low.
Failed conditions
[67.5% Coverage on New Code](https://sonarcloud.io/component_measures?id=molgenis_vip-report&pullRequest=143&metric=new_coverage&view=list) (required ≥ 80%)
| @@ -33,10 +33,14 @@ usage: java -jar vcf-report.jar -i <arg> [-o <arg>] [-f] [-t <arg>] [-pb | |||
| -g,--genes <arg> Genes file to be used as reference track in the | |||
| genome browser, UCSC NCBI RefSeq GFF file | |||
| (gff.gz or gff3.gz). | |||
| -c,--cram <arg> Comma-separated list of sample-bam files | |||
| -c,--cram <arg> Comma-separated list of sample-cram files | |||
| } | ||
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| private static boolean isFeature(List<ContigInterval> contigIntervals, BedmethylLine bedmethylLine) { | ||
| for (ContigInterval contigInterval : contigIntervals) { |
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a more efficient solution would be to create a map from Contig to ContigInterval before looping through .bed lines. this would speed up the slicing of the bedmethyl
| return false; | ||
| } | ||
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| private static boolean isOverlappingFeature(BedmethylLine bedmethylLine, ContigInterval contigInterval) { |
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would have been nice to refactor the code copied from GenesFilter.java in order to reuse this method.
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