public class SamFileValidator
extends java.lang.Object
SAMRecord.isValid()
Modifier and Type | Class and Description |
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static class |
SamFileValidator.ValidationMetrics |
Constructor and Description |
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SamFileValidator(java.io.PrintWriter out,
int maxTempFiles) |
Modifier and Type | Method and Description |
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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) |
SamFileValidator |
setValidateIndex(boolean validateIndex)
Deprecated.
use setIndexValidationStringency 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.
|
public SamFileValidator(java.io.PrintWriter out, int maxTempFiles)
public void setErrorsToIgnore(java.util.Collection<SAMValidationError.Type> types)
public void setIgnoreWarnings(boolean ignoreWarnings)
public boolean validateSamFileSummary(SamReader samReader, ReferenceSequenceFile reference)
samReader
- records to validatereference
- if null, NM tag validation is skippedpublic boolean validateSamFileVerbose(SamReader samReader, ReferenceSequenceFile reference)
samReader
- records to validatereference
- if null, NM tag validation is skipped
processing will stop after this threshold has been reachedpublic void validateBamFileTermination(java.io.File inputFile)
public void setVerbose(boolean verbose, int maxVerboseOutput)
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.public boolean isBisulfiteSequenced()
public void setBisulfiteSequenced(boolean bisulfiteSequenced)
public SamFileValidator setValidateIndex(boolean validateIndex)
public SamFileValidator setIndexValidationStringency(BamIndexValidator.IndexValidationStringency stringency)