Class CoordinateSortingChecker
- java.lang.Object
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- de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker
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- All Implemented Interfaces:
VariantContextProcessor
,Closeable
,AutoCloseable
public class CoordinateSortingChecker extends Object implements VariantContextProcessor
Check that the VCF file is sorted by coordinateSince VCF files do not have to provide a reference name dictionary in their header, validating the sort order of the chromosomes is tricky. Instead, we check that there is no run of VCF records for a chromosome, something on a different chromsome, and then a previous one again. Within one chromosome, we check by change begin position.
In case of problems,
put(htsjdk.variant.variantcontext.VariantContext)
throws aVariantContextFilterException
.- Author:
- Manuel Holtgrewe
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Constructor Summary
Constructors Constructor Description CoordinateSortingChecker(VariantContextProcessor sink)
Initialize the checker
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Mark processing as done, no more variants will come in.void
put(htsjdk.variant.variantcontext.VariantContext vc)
Put a Variant Context into the filter.
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Constructor Detail
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CoordinateSortingChecker
public CoordinateSortingChecker(VariantContextProcessor sink)
Initialize the checker
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Method Detail
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put
public void put(htsjdk.variant.variantcontext.VariantContext vc) throws VariantContextFilterException
Description copied from interface:VariantContextProcessor
Put a Variant Context into the filter.- Specified by:
put
in interfaceVariantContextProcessor
- Parameters:
vc
-VariantContext
to put into the filter.- Throws:
VariantContextFilterException
- on problems during the filtration
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close
public void close()
Description copied from interface:VariantContextProcessor
Mark processing as done, no more variants will come in.- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfaceVariantContextProcessor
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