OrderedPairReader

gngs.OrderedPairReader

All Implemented Interfaces and Traits:

java.io.Closeable
```
@groovy.transform.CompileStatic
class OrderedPairReader
extends java.lang.Object
implements java.io.Closeable
```
A utility class for efficiently iterating all the read pairs in a BAM file.
NOTE: unpaired and chimeric reads are omitted
Performance depends on buffering a window of reads so that the mates for each read are encountered within the buffer and thus random lookup of mates is not needed. The right size for it depends on the coverage depth and the separation between paired reads. It should be able to hold enough reads that most of the time a read's pair is encountered before the buffer overflows. When it overflows the loop below starts doing random queries (slow) to resolve the mates for reads so that the pair can be output together. See the spoolSize option which can be passed to the constructor.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`java.util.concurrent.atomic.AtomicInteger`	`asyncRequests`
`java.util.concurrent.atomic.AtomicInteger`	`asyncResolves`
`SAM`	`bam`
`java.util.Set<java.lang.String>`	`chimericPreprocessedReads` To contain memory consumption, preprocessed reads are cleared every chromosome.
`java.lang.String`	`currentChr`
`gngs.Region`	`currentRegion`
`java.lang.String`	`debugRead`
`int`	`forcedQueries`
`gngs.ReadMateLookupActor`	`forcedQueryLookupActor`
`boolean`	`includeChimeric`
`boolean`	`includeUnmapped`
`java.util.logging.Logger`	`log`
`java.util.List<gngs.ReadMateLookupActor>`	`lookupActors`
`int`	`lookupConcurrency`
`int`	`lookupReaderIndex`
`int`	`maxSpoolSize`
`gngs.MissingMateIndex`	`missingMates`
`int`	`pairs`
`java.util.Set<java.lang.String>`	`preprocessedReads`
`ProgressCounter`	`progress`
`htsjdk.samtools.SamReader`	`randomLookupReader`
`java.util.List<AsyncMateResolveWorker>`	`resolvers`
`java.lang.String`	`sample`
`int`	`unpairedReads`
`boolean`	`verbose`
`java.util.List<gngs.SAMRecordPair>`	`writeSpool` List of reads in order that need to be written out

Constructor Summary

Constructors
Constructor and description
`OrderedPairReader (java.util.Map options, SAM sam)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`void`	`addPreprocessedRead(gngs.SAMRecordPair pair)`
	`void`	`close()`
	`void`	`eachPair(groovy.lang.Closure c)`
	`void`	`eachPair(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)`
	`void`	`eachPair(Regions regions, groovy.lang.Closure c)`
	`void`	`eachPairImpl(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)`
	`void`	`flushSpooledReads(groovy.lang.Closure c)`
	`void`	`forceQueryOverflowRead(int position)`
	`boolean`	`isNewChromosome(htsjdk.samtools.SAMRecord record)`
	`boolean`	`isProcessableRead(htsjdk.samtools.SAMRecord record)`
	`void`	`processPartneredReads(groovy.lang.Closure c)`
	`htsjdk.samtools.SAMRecord`	`queryMateByDirectLookup(htsjdk.samtools.SAMRecord record)`
	`boolean`	`resolveAsynchronously(gngs.SAMRecordPair pair)`
	`void`	`scheduleAsyncResolves()`
	`java.util.Map`	`spoolStats()`

Inherited Methods Summary

Inherited Methods
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()`

- Property Detail
  - java.util.concurrent.atomic.AtomicInteger asyncRequests
  - java.util.concurrent.atomic.AtomicInteger asyncResolves
  - SAM bam
  - java.util.Set<java.lang.String> chimericPreprocessedReads
    
    To contain memory consumption, preprocessed reads are cleared every chromosome. We can't, however, do that for chimeric reads since they span chromosomes
  - java.lang.String currentChr
  - gngs.Region currentRegion
  - java.lang.String debugRead
  - int forcedQueries
  - gngs.ReadMateLookupActor forcedQueryLookupActor
  - boolean includeChimeric
  - boolean includeUnmapped
  - java.util.logging.Logger log
  - java.util.List<gngs.ReadMateLookupActor> lookupActors
  - int lookupConcurrency
  - int lookupReaderIndex
  - final int maxSpoolSize
  - gngs.MissingMateIndex missingMates
  - int pairs
  - java.util.Set<java.lang.String> preprocessedReads
  - ProgressCounter progress
  - htsjdk.samtools.SamReader randomLookupReader
  - java.util.List<AsyncMateResolveWorker> resolvers
  - java.lang.String sample
  - int unpairedReads
  - boolean verbose
  - java.util.List<gngs.SAMRecordPair> writeSpool
    
    List of reads in order that need to be written out
- Constructor Detail
  - OrderedPairReader(java.util.Map options, SAM sam)
- Method Detail
  - void addPreprocessedRead(gngs.SAMRecordPair pair)
  - @java.lang.Override void close()
  - void eachPair(groovy.lang.Closure c)
  - void eachPair(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic void eachPair(Regions regions, groovy.lang.Closure c)
  - void eachPairImpl(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)
  - void flushSpooledReads(groovy.lang.Closure c)
  - void forceQueryOverflowRead(int position)
  - boolean isNewChromosome(htsjdk.samtools.SAMRecord record)
  - boolean isProcessableRead(htsjdk.samtools.SAMRecord record)
  - @groovy.transform.CompileStatic void processPartneredReads(groovy.lang.Closure c)
  - htsjdk.samtools.SAMRecord queryMateByDirectLookup(htsjdk.samtools.SAMRecord record)
  - boolean resolveAsynchronously(gngs.SAMRecordPair pair)
  - void scheduleAsyncResolves()
  - @groovy.transform.CompileStatic java.util.Map spoolStats()

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class OrderedPairReader

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

java.util.concurrent.atomic.AtomicInteger asyncRequests

java.util.concurrent.atomic.AtomicInteger asyncResolves

SAM bam

java.util.Set<java.lang.String> chimericPreprocessedReads

java.lang.String currentChr

gngs.Region currentRegion

java.lang.String debugRead

int forcedQueries

gngs.ReadMateLookupActor forcedQueryLookupActor

boolean includeChimeric

boolean includeUnmapped

java.util.logging.Logger log

java.util.List<gngs.ReadMateLookupActor> lookupActors

int lookupConcurrency

int lookupReaderIndex

final int maxSpoolSize

gngs.MissingMateIndex missingMates

int pairs

java.util.Set<java.lang.String> preprocessedReads

ProgressCounter progress

htsjdk.samtools.SamReader randomLookupReader

java.util.List<AsyncMateResolveWorker> resolvers

java.lang.String sample

int unpairedReads

boolean verbose

java.util.List<gngs.SAMRecordPair> writeSpool

Constructor Detail

OrderedPairReader(java.util.Map options, SAM sam)

Method Detail

void addPreprocessedRead(gngs.SAMRecordPair pair)

@java.lang.Override void close()

void eachPair(groovy.lang.Closure c)

void eachPair(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachPair(Regions regions, groovy.lang.Closure c)

void eachPairImpl(htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)

void flushSpooledReads(groovy.lang.Closure c)

void forceQueryOverflowRead(int position)

boolean isNewChromosome(htsjdk.samtools.SAMRecord record)

boolean isProcessableRead(htsjdk.samtools.SAMRecord record)

@groovy.transform.CompileStatic void processPartneredReads(groovy.lang.Closure c)

htsjdk.samtools.SAMRecord queryMateByDirectLookup(htsjdk.samtools.SAMRecord record)

boolean resolveAsynchronously(gngs.SAMRecordPair pair)

void scheduleAsyncResolves()

@groovy.transform.CompileStatic java.util.Map spoolStats()