@groovy.transform.CompileStatic class OrderedPairWriter extends java.lang.Object implements java.io.Closeable
When processing reads as pairs it can be tricky to write them out again while maintaining the order expected for a "sorted" BAM file. This class buffers the second read until the next R1 is output that would violate the second read's sort order. Note: Currently this class filters out chimeric reads since ordering them is particularly tricky.
| Type | Name and description |
|---|---|
java.util.TreeSet<gngs.SAMRecordPair> |
buffer |
int |
currentReferenceIndex |
ProgressCounter |
progress |
htsjdk.samtools.SAMFileWriter |
samWriter |
boolean |
verbose |
int |
written |
| Constructor and description |
|---|
OrderedPairWriter
(htsjdk.samtools.SAMFileWriter w) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
void |
addAlignmentPair(gngs.SAMRecordPair pair) |
|
void |
close() |
|
void |
flushBuffer() |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Groovy Documentation