htsjdk.samtools

Class SamFileValidator

java.lang.Object

htsjdk.samtools.SamFileValidator

public class SamFileValidator
extends java.lang.Object

Validates SAM files as follows:

• checks sam file header for sequence dictionary
• checks sam file header for read groups
• for each sam record
  • reports error detected by SAMRecord.isValid()
  • validates NM (nucleotide differences) exists and matches reality
  • validates mate fields agree with data in the mate record

See Also:

SAMRecord.isValid()

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SamFileValidator.ValidationMetrics

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_QUALITY_NOT_STORED_ERRORS

Constructor Summary

Constructors

Constructor and Description
SamFileValidator(java.io.PrintWriter out, int maxTempFiles)

Method Summary

Modifier and Type	Method and Description
int	getNumErrors() Number of errors during SAM file validation
int	getNumWarnings() Number of warnings during SAM file validation
boolean	getSkipMateValidation()
boolean	isBisulfiteSequenced()
void	setBisulfiteSequenced(boolean bisulfiteSequenced)
void	setErrorsToIgnore(java.util.Collection<SAMValidationError.Type> types) Sets one or more error types that should not be reported on.
void	setIgnoreWarnings(boolean ignoreWarnings)
SamFileValidator	setIndexValidationStringency(BamIndexValidator.IndexValidationStringency stringency)
void	setSkipMateValidation(boolean skipMateValidation) Sets whether or not we should run mate validation beyond the mate cigar check, which is useful in extreme edge cases that would require a lot of memory to do the validation.
SamFileValidator	setValidateIndex(boolean validateIndex) Deprecated. use setIndexValidationStringency(htsjdk.samtools.BamIndexValidator.IndexValidationStringency) instead
void	setVerbose(boolean verbose, int maxVerboseOutput) Control verbosity
void	validateBamFileTermination(java.io.File inputFile)
boolean	validateSamFileSummary(SamReader samReader, ReferenceSequenceFile reference) Outputs validation summary report to out.
boolean	validateSamFileVerbose(SamReader samReader, ReferenceSequenceFile reference) Outputs validation error details to out.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_QUALITY_NOT_STORED_ERRORS

public static final int MAX_QUALITY_NOT_STORED_ERRORS

See Also:

Constant Field Values

Constructor Detail

SamFileValidator

public SamFileValidator(java.io.PrintWriter out,
                        int maxTempFiles)

Method Detail

setErrorsToIgnore

public void setErrorsToIgnore(java.util.Collection<SAMValidationError.Type> types)

Sets one or more error types that should not be reported on.

setIgnoreWarnings

public void setIgnoreWarnings(boolean ignoreWarnings)

setSkipMateValidation

public void setSkipMateValidation(boolean skipMateValidation)

Sets whether or not we should run mate validation beyond the mate cigar check, which is useful in extreme edge cases that would require a lot of memory to do the validation.

Parameters:

skipMateValidation - should this tool skip mate validation

getSkipMateValidation

public boolean getSkipMateValidation()

Returns:

true if the validator will skip mate validation, otherwise false

validateSamFileSummary

public boolean validateSamFileSummary(SamReader samReader,
                                      ReferenceSequenceFile reference)

Outputs validation summary report to out.

Parameters:

samReader - records to validate

reference - if null, NM tag validation is skipped

Returns:

boolean true if there are no validation errors, otherwise false

validateSamFileVerbose

public boolean validateSamFileVerbose(SamReader samReader,
                                      ReferenceSequenceFile reference)

Outputs validation error details to out.

Parameters:

samReader - records to validate

reference - if null, NM tag validation is skipped processing will stop after this threshold has been reached

Returns:

boolean true if there are no validation errors, otherwise false

validateBamFileTermination

public void validateBamFileTermination(java.io.File inputFile)

getNumWarnings

public int getNumWarnings()

Number of warnings during SAM file validation

Returns:

number of warnings

getNumErrors

public int getNumErrors()

Number of errors during SAM file validation

Returns:

number of errors

setVerbose

public void setVerbose(boolean verbose,
                       int maxVerboseOutput)

Control verbosity

Parameters:

verbose - True in order to emit a message per error or warning.

maxVerboseOutput - If verbose, emit no more than this many messages. Ignored if !verbose.

isBisulfiteSequenced

public boolean isBisulfiteSequenced()

setBisulfiteSequenced

public void setBisulfiteSequenced(boolean bisulfiteSequenced)

setValidateIndex

@Deprecated
public SamFileValidator setValidateIndex(boolean validateIndex)

Deprecated. use setIndexValidationStringency(htsjdk.samtools.BamIndexValidator.IndexValidationStringency) instead

setIndexValidationStringency

public SamFileValidator setIndexValidationStringency(BamIndexValidator.IndexValidationStringency stringency)