picard.sam

Class ValidateSamFile

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ValidateSamFile

public class ValidateSamFile
extends CommandLineProgram

Command line program wrapping SamFileValidator.

Author:

Doug Voet

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ValidateSamFile.Mode

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<htsjdk.samtools.SAMValidationError.Type>	IGNORE
boolean	IGNORE_WARNINGS
htsjdk.samtools.BamIndexValidator.IndexValidationStringency	INDEX_VALIDATION_STRINGENCY
java.io.File	INPUT
boolean	IS_BISULFITE_SEQUENCED
int	MAX_OPEN_TEMP_FILES
java.lang.Integer	MAX_OUTPUT
ValidateSamFile.Mode	MODE
java.io.File	OUTPUT
boolean	VALIDATE_INDEX

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
ValidateSamFile()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

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

INPUT

@Option(shortName="I",
        doc="Input SAM/BAM file")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Output file or standard out if missing",
        optional=true)
public java.io.File OUTPUT

MODE

@Option(shortName="M",
        doc="Mode of output")
public ValidateSamFile.Mode MODE

IGNORE

@Option(doc="List of validation error types to ignore.")
public java.util.List<htsjdk.samtools.SAMValidationError.Type> IGNORE

MAX_OUTPUT

@Option(shortName="MO",
        doc="The maximum number of lines output in verbose mode")
public java.lang.Integer MAX_OUTPUT

IGNORE_WARNINGS

@Option(doc="If true, only report errors and ignore warnings.")
public boolean IGNORE_WARNINGS

VALIDATE_INDEX

@Option(doc="DEPRECATED.  Use INDEX_VALIDATION_STRINGENCY instead.  If true and input is a BAM file with an index file, also validates the index.  Until this parameter is retired VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.")
public boolean VALIDATE_INDEX

INDEX_VALIDATION_STRINGENCY

@Option(doc="If set to anything other than IndexValidationStringency.NONE and input is a BAM file with an index file, also validates the index at the specified stringency. Until VALIDATE_INDEX is retired, VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.")
public htsjdk.samtools.BamIndexValidator.IndexValidationStringency INDEX_VALIDATION_STRINGENCY

IS_BISULFITE_SEQUENCED

@Option(shortName="BISULFITE",
        doc="Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as an error in computing the value of the NM tag.")
public boolean IS_BISULFITE_SEQUENCED

MAX_OPEN_TEMP_FILES

@Option(doc="Relevant for a coordinate-sorted file containing read pairs only. Maximum number of file handles to keep open when spilling mate info to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the \'ulimit -n\' command on a Unix system.")
public int MAX_OPEN_TEMP_FILES

Constructor Detail

ValidateSamFile

public ValidateSamFile()

Method Detail

main

public static void main(java.lang.String[] args)

doWork

protected int doWork()

Description copied from class: CommandLineProgram

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.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.