CollectAlignmentSummaryMetrics (picard 2.8.1 API)

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

```
public class CollectAlignmentSummaryMetrics
extends SinglePassSamProgram
```
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment. Metrics to include, but not limited to:
- Total number of reads (total, period, no exclusions)
- Total number of PF reads (PF == does not fail vendor check flag)
- Number of PF noise reads (does not fail vendor check and has noise attr set)
- Total aligned PF reads (any PF read that has a sequence and position)
- High quality aligned PF reads (high quality == mapping quality >= 20)
- High quality aligned PF bases (actual aligned bases, calculate off alignment blocks)
- High quality aligned PF Q20 bases (subset of above where base quality >= 20)
- Median mismatches in HQ aligned PF reads (how many aligned bases != ref on average)
- Reads aligned in pairs (vs. reads aligned with mate unaligned/not present)
- Read length (how to handle mixed lengths?)
- Bad Cycles - how many machine cycles yielded combined no-call and mismatch rates of >= 80%
- Strand balance - reads mapped to positive strand / total mapped reads
Metrics are written for the first read of a pair, the second read, and combined for the pair. Chimeras are identified if any of the of following criteria are met:
- the insert size is larger than MAX_INSERT_SIZE
- the ends of a pair map to different contigs
- the paired end orientation is different that the expected orientation
- the read contains an SA tag (chimeric alignment)

Field Summary

Fields
Modifier and Type	Field	Description
`List<String>`	`ADAPTER_SEQUENCE`
`Set<htsjdk.samtools.SamPairUtil.PairOrientation>`	`EXPECTED_PAIR_ORIENTATIONS`
`boolean`	`IS_BISULFITE_SEQUENCED`
`int`	`MAX_INSERT_SIZE`
`Set<MetricAccumulationLevel>`	`METRIC_ACCUMULATION_LEVEL`
`File`	`REFERENCE_SEQUENCE`

Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Constructor Summary

Constructors
Constructor Description

CollectAlignmentSummaryMetrics()

Constructors
Constructor	Description
`CollectAlignmentSummaryMetrics()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)`	Should be implemented by subclasses to accept SAMRecords one at a time.
`protected void`	`finish()`	Should be implemented by subclasses to do one-time finalization work.
`static void`	`main(String[] argv)`	Required main method implementation.
`protected void`	`setup(htsjdk.samtools.SAMFileHeader header, File samFile)`	Should be implemented by subclasses to do one-time initialization work.
`protected int`	`testDoWork()`	Silly method that is necessary to give unit test access to call doWork()

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

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

Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, makeItSo, usesNoRefReads

Field Detail

MAX_INSERT_SIZE

@Option(doc="Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs.")
public int MAX_INSERT_SIZE

EXPECTED_PAIR_ORIENTATIONS

@Option(doc="Paired-end reads that do not have this expected orientation will be considered chimeric.")
public Set<htsjdk.samtools.SamPairUtil.PairOrientation> EXPECTED_PAIR_ORIENTATIONS

ADAPTER_SEQUENCE

@Option(doc="List of adapter sequences to use when processing the alignment metrics.")
public List<String> ADAPTER_SEQUENCE

METRIC_ACCUMULATION_LEVEL

@Option(shortName="LEVEL",
        doc="The level(s) at which to accumulate metrics.")
public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

IS_BISULFITE_SEQUENCED

@Option(shortName="BS",
        doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.")
public boolean IS_BISULFITE_SEQUENCED

REFERENCE_SEQUENCE

@Option(shortName="R",
        doc="Reference sequence file. Note that while this argument isn\'t required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.",
        optional=true,
        overridable=true)
public File REFERENCE_SEQUENCE

Constructor Detail
- CollectAlignmentSummaryMetrics
```
public CollectAlignmentSummaryMetrics()
```

Method Detail
- main
```
public static void main(String[] argv)
```
  Required main method implementation.
- testDoWork
```
protected final int testDoWork()
```
  Silly method that is necessary to give unit test access to call doWork()
- setup
```
protected void setup(htsjdk.samtools.SAMFileHeader header,
                     File samFile)
```
  Description copied from class: SinglePassSamProgram
  
  Should be implemented by subclasses to do one-time initialization work.
  
  Specified by:
  
  setup in class SinglePassSamProgram
- acceptRead
```
protected void acceptRead(htsjdk.samtools.SAMRecord rec,
                          htsjdk.samtools.reference.ReferenceSequence ref)
```
  Description copied from class: SinglePassSamProgram
  
  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.
  
  Specified by:
  
  acceptRead in class SinglePassSamProgram
- finish
```
protected void finish()
```
  Description copied from class: SinglePassSamProgram
  
  Should be implemented by subclasses to do one-time finalization work.
  
  Specified by:
  
  finish in class SinglePassSamProgram

Class CollectAlignmentSummaryMetrics

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Fields inherited from class picard.analysis.SinglePassSamProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Methods inherited from class picard.analysis.SinglePassSamProgram

Field Detail

MAX_INSERT_SIZE

EXPECTED_PAIR_ORIENTATIONS

ADAPTER_SEQUENCE

METRIC_ACCUMULATION_LEVEL

IS_BISULFITE_SEQUENCED

REFERENCE_SEQUENCE

Constructor Detail

CollectAlignmentSummaryMetrics

Method Detail

main

testDoWork

setup

acceptRead

finish