ALS-7737: Better support for splitting genomic data by chromosome #137
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…data in a similar fashion
ramari16
added
bug
ramari16
commented
Feb 27, 2025
| @@ -159,7 +159,11 @@ public Set<String> filterVariantSetForPatientSet(Set<String> variantSet, Collect | |||
| String bucketKey = variantSpec.split(",")[0] + ":" + (Integer.parseInt(variantSpec.split(",")[1])/1000); | |||
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| //testBit uses inverted indexes include +2 offset for bookends | |||
| return _bucketMask.testBit(maxIndex - Collections.binarySearch(bucketList, bucketKey) + 2); | |||
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This bug has existed since forever. testBit(-1) was sometimes returning not false because of overflows
ramari16
commented
Feb 27, 2025
| import java.io.IOException; | ||
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| import static edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader.convertInfoStoresToByteIndexed; | ||
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| public class ReSplitMergeInfoStores { |
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I don't think this is used, will verify and delete
ramari16
commented
Feb 27, 2025
| @@ -22,57 +22,77 @@ | |||
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| public class NewVCFLoader { | |||
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All changes in this file are to support extending it and removing all the static nonsense
ramari16
commented
Feb 27, 2025
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| private static final Joiner COMMA_JOINER = Joiner.on(","); | ||
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| public VCFIndexBuilder(File vcfPatientMappingFile, File patientUUIDToIdMappingFile, File vcfIndexOutputDirectory, Set<String> validPatientType) { |
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This is a BCH specific utility class. I will add some documentation to explain exactly the inputs to create a vcf file but I doubt it will be useful for anyone else
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This PR adds better support for building a genomic dataset split by chromosome. Previously, in BDC, we ran the
NewVCFLoaderfor each chromosome, which was not as efficient and would be even less so as we move to running jobs in docker containers.This new functionality allows us to pass a single VCF index file to
SplitChromosomeVcfLoaderand it will process all VCFs in it and store the genomic dataset in appropriate directories split by chromosome. A similar approach was done forSplitChromosomeVariantMetadataLoader.Integration tests were also updated to use the implementation of
GenomicProcessorusing a split-chromosome dataset. This uncovered several small bugs which are fixed in this PR