picard.sam

Class CompareSAMs

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.CompareSAMs

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.

Author:

alecw@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.io.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, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CompareSAMs()

Method Summary

Modifier and Type	Method and 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(java.lang.String[] argv)

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

Field Detail

samFiles

@PositionalArguments(minElements=2,
                     maxElements=2)
public java.util.List<java.io.File> samFiles

Constructor Detail

CompareSAMs

public CompareSAMs()

Method Detail

main

public static void main(java.lang.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()