public class SamFileValidator extends Object
SAMRecord.isValid()
Modifier and Type | Class | Description |
---|---|---|
static class |
SamFileValidator.ValidationMetrics |
Modifier and Type | Field | Description |
---|---|---|
static int |
MAX_QUALITY_NOT_STORED_ERRORS |
Constructor | Description |
---|---|
SamFileValidator(PrintWriter out,
int maxTempFiles) |
Modifier and Type | Method | 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(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.
|
void |
setVerbose(boolean verbose,
int maxVerboseOutput) |
Control verbosity
|
void |
validateBamFileTermination(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 static final int MAX_QUALITY_NOT_STORED_ERRORS
public SamFileValidator(PrintWriter out, int maxTempFiles)
public void setErrorsToIgnore(Collection<SAMValidationError.Type> types)
public void setIgnoreWarnings(boolean ignoreWarnings)
public void setSkipMateValidation(boolean skipMateValidation)
skipMateValidation
- should this tool skip mate validationpublic boolean getSkipMateValidation()
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(File inputFile)
public int getNumWarnings()
public int getNumErrors()
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)
@Deprecated public SamFileValidator setValidateIndex(boolean validateIndex)
public SamFileValidator setIndexValidationStringency(BamIndexValidator.IndexValidationStringency stringency)