SinglePassSamProgram (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.analysis.SinglePassSamProgram

Direct Known Subclasses:

CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectInsertSizeMetrics, CollectQualityYieldMetrics, CollectRnaSeqMetrics, CollectSequencingArtifactMetrics, MeanQualityByCycle, QualityScoreDistribution
```
public abstract class SinglePassSamProgram
extends CommandLineProgram
```
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.

Field Summary

Fields
Modifier and Type Field Description

boolean ASSUME_SORTED

File INPUT

File OUTPUT

long STOP_AFTER
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field	Description
`boolean`	`ASSUME_SORTED`
`File`	`INPUT`
`File`	`OUTPUT`
`long`	`STOP_AFTER`

Constructor Summary

Constructors
Constructor Description

SinglePassSamProgram()

Constructors
Constructor	Description
`SinglePassSamProgram()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected abstract void`	`acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)`	Should be implemented by subclasses to accept SAMRecords one at a time.
`protected int`	`doWork()`	Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
`protected abstract void`	`finish()`	Should be implemented by subclasses to do one-time finalization work.
`static void`	`makeItSo(File input, File referenceSequence, boolean assumeSorted, long stopAfter, Collection<SinglePassSamProgram> programs)`
`void`	`setReferenceSequence(File referenceFile)`	Set the reference File.
`protected abstract void`	`setup(htsjdk.samtools.SAMFileHeader header, File samFile)`	Should be implemented by subclasses to do one-time initialization work.
`protected boolean`	`usesNoRefReads()`	Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input SAM or BAM file.")
public File INPUT

OUTPUT

@Argument(shortName="O",
          doc="File to write the output to.")
public File OUTPUT

ASSUME_SORTED

@Argument(doc="If true (default), then the sort order in the header file will be ignored.",
          shortName="AS")
public boolean ASSUME_SORTED

STOP_AFTER

@Argument(doc="Stop after processing N reads, mainly for debugging.")
public long STOP_AFTER

Constructor Detail
- SinglePassSamProgram
```
public SinglePassSamProgram()
```

Method Detail
- setReferenceSequence
```
public void setReferenceSequence(File referenceFile)
```
  Set the reference File.
- doWork
```
protected final int doWork()
```
  Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
  
  Specified by:
  
  doWork in class CommandLineProgram
  
  Returns:
  
  program exit status.
- makeItSo
```
public static void makeItSo(File input,
                            File referenceSequence,
                            boolean assumeSorted,
                            long stopAfter,
                            Collection<SinglePassSamProgram> programs)
```
- usesNoRefReads
```
protected boolean usesNoRefReads()
```
  Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
- setup
```
protected abstract void setup(htsjdk.samtools.SAMFileHeader header,
                              File samFile)
```
  Should be implemented by subclasses to do one-time initialization work.
- acceptRead
```
protected abstract void acceptRead(htsjdk.samtools.SAMRecord rec,
                                   htsjdk.samtools.reference.ReferenceSequence ref)
```
  Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.
- finish
```
protected abstract void finish()
```
  Should be implemented by subclasses to do one-time finalization work.

Class SinglePassSamProgram

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

ASSUME_SORTED

STOP_AFTER

Constructor Detail

SinglePassSamProgram

Method Detail

setReferenceSequence

doWork

makeItSo

usesNoRefReads

setup

acceptRead

finish