CompareSAMs (picard 2.18.2 API)

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java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.sam.CompareSAMs

```
@DocumentedFeature
public class CompareSAMs
extends CommandLineProgram
```
Rudimentary SAM comparer. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info. Summarizes the number of alignments that match, mismatch, are missing, etc.

Field Summary

Fields
Modifier and Type Field Description

List<File> samFiles
- 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

Constructor Summary

Constructors
Constructor Description

CompareSAMs()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`areEqual()`
`protected int`	`doWork()`	Do the work after command line has been parsed.
`int`	`getMappingsDiffer()`
`int`	`getMappingsMatch()`
`int`	`getMissingLeft()`
`int`	`getMissingRight()`
`int`	`getUnmappedBoth()`
`int`	`getUnmappedLeft()`
`int`	`getUnmappedRight()`
`static void`	`main(String[] argv)`

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

samFiles

@PositionalArguments(minElements=2,
                     maxElements=2)
public List<File> samFiles

Constructor Detail
- CompareSAMs
```
public CompareSAMs()
```

Method Detail
- main
```
public static void main(String[] argv)
```
- doWork
```
protected int doWork()
```
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
  
  Specified by:
  
  doWork in class CommandLineProgram
  
  Returns:
  
  program exit status.
- getMappingsMatch
```
public int getMappingsMatch()
```
- getUnmappedBoth
```
public int getUnmappedBoth()
```
- getUnmappedLeft
```
public int getUnmappedLeft()
```
- getUnmappedRight
```
public int getUnmappedRight()
```
- getMappingsDiffer
```
public int getMappingsDiffer()
```
- getMissingLeft
```
public int getMissingLeft()
```
- getMissingRight
```
public int getMissingRight()
```
- areEqual
```
public boolean areEqual()
```

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