Package picard.sam.markduplicates.util
Class PhysicalLocationForMateCigarSet
- java.lang.Object
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- picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
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public class PhysicalLocationForMateCigarSet extends Object
This stores records that are comparable for detecting optical duplicates.
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Constructor Summary
Constructors Constructor Description PhysicalLocationForMateCigarSet()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(ReadEndsForMateCigar end)
Adds the end to this set, if not already added based on physical locationSet<ReadEnds>
getReadEnds()
Gets the set of read endsvoid
remove(ReadEndsForMateCigar end)
Removes the end from this set, if presentvoid
replace(ReadEndsForMateCigar current, ReadEndsForMateCigar other)
Replaces a given end with the other end.int
size()
The number of records in this set
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Method Detail
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add
public void add(ReadEndsForMateCigar end)
Adds the end to this set, if not already added based on physical location
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size
public int size()
The number of records in this set
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remove
public void remove(ReadEndsForMateCigar end)
Removes the end from this set, if present
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replace
public void replace(ReadEndsForMateCigar current, ReadEndsForMateCigar other)
Replaces a given end with the other end. This ensures that that current is in this set
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