Package picard.sam

Class ReplaceSamHeader

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ReplaceSamHeader

@DocumentedFeature
public class ReplaceSamHeader
extends CommandLineProgram

Field Summary

Fields

Modifier and Type	Field	Description
File	HEADER
File	INPUT
File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
ReplaceSamHeader()

Method Summary

Modifier and Type	Method	Description
protected int	doWork()	Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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 Details

INPUT

@Argument(doc="SAM/BAM/CRAM file from which SAMRecords will be read.",
          shortName="I")
public File INPUT

HEADER

@Argument(doc="SAM/BAM/CRAM file from which SAMFileHeader will be read.")
public File HEADER

OUTPUT

@Argument(doc="header from HEADER file will be written to this file, followed by records from INPUT file",
          shortName="O")
public File OUTPUT

Constructor Details

ReplaceSamHeader

public ReplaceSamHeader()

Method Details

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.