public class VariantContextComparator extends Object implements Comparator<VariantContext>, Serializable
Constructor and Description |
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VariantContextComparator(Collection<VCFContigHeaderLine> headerLines)
Creates a VariantContextComparator from the given VCF contig header lines.
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VariantContextComparator(List<String> contigs) |
VariantContextComparator(SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
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int |
compare(VariantContext firstVariantContext,
VariantContext secondVariantContext) |
static List<String> |
getSequenceNameList(SAMSequenceDictionary dictionary) |
boolean |
isCompatible(Collection<VCFContigHeaderLine> headerLines)
Returns true if the given header lines are from a file sorted according to this VariantContextComparator.
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
comparing, comparing, comparingDouble, comparingInt, comparingLong, equals, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong
public VariantContextComparator(Collection<VCFContigHeaderLine> headerLines)
public VariantContextComparator(SAMSequenceDictionary dictionary)
public static List<String> getSequenceNameList(SAMSequenceDictionary dictionary)
public int compare(VariantContext firstVariantContext, VariantContext secondVariantContext)
compare
in interface Comparator<VariantContext>
public boolean isCompatible(Collection<VCFContigHeaderLine> headerLines)