public class DuplicateSet
extends java.lang.Object
Constructor and Description |
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DuplicateSet()
Sets the duplicate flag by default
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DuplicateSet(boolean setDuplicateFlag) |
DuplicateSet(boolean setDuplicateFlag,
SAMRecordDuplicateComparator comparator) |
DuplicateSet(SAMRecordDuplicateComparator comparator) |
Modifier and Type | Method and Description |
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int |
add(SAMRecord record)
Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set.
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java.util.List<SAMRecord> |
getRecords()
Gets the list of records from this set.
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java.util.List<SAMRecord> |
getRecords(boolean sort)
Gets the list of records from this set.
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SAMRecord |
getRepresentative()
Gets the representative record according to the duplicate comparator.
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boolean |
isEmpty() |
int |
numDuplicates()
Returns the number of duplicates in this set, including the representative record.
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void |
setDuplicateFlag(boolean setDuplicateFlag)
Controls if we should update the duplicate flag of the records in this set.
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int |
size()
Returns the number of records in this set.
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public DuplicateSet()
public DuplicateSet(boolean setDuplicateFlag)
public DuplicateSet(SAMRecordDuplicateComparator comparator)
public DuplicateSet(boolean setDuplicateFlag, SAMRecordDuplicateComparator comparator)
public int add(SAMRecord record)
record
- the record to add.public java.util.List<SAMRecord> getRecords(boolean sort)
sort
- true if we want the records in the duplicate set sorted by duplicate order, false if we do not care about the order.public java.util.List<SAMRecord> getRecords()
public SAMRecord getRepresentative()
public int size()
public int numDuplicates()
public boolean isEmpty()
public void setDuplicateFlag(boolean setDuplicateFlag)