Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.sra |
Modifier and Type | Method and Description |
---|---|
java.util.List<SAMValidationError> |
SAMFileHeader.getValidationErrors() |
java.util.List<SAMValidationError> |
SAMRecord.isValid()
Perform various validations of SAMRecord.
|
java.util.List<SAMValidationError> |
SAMRecord.isValid(boolean firstOnly)
Perform various validations of SAMRecord.
|
java.util.List<SAMValidationError> |
Cigar.isValid(java.lang.String readName,
long recordNumber)
Exhaustive validation of CIGAR.
|
java.util.List<SAMValidationError> |
SAMRecord.validateCigar(long recordNumber)
Run all validations of CIGAR.
|
static java.util.List<SAMValidationError> |
SAMUtils.validateCigar(SAMRecord rec,
Cigar cigar,
java.lang.Integer referenceIndex,
java.util.List<AlignmentBlock> alignmentBlocks,
long recordNumber,
java.lang.String cigarTypeName)
Run all validations of the mate's CIGAR.
|
static java.util.List<SAMValidationError> |
SAMUtils.validateMateCigar(SAMRecord rec,
long recordNumber)
Run all validations of the mate's CIGAR.
|
Modifier and Type | Method and Description |
---|---|
void |
SAMFileHeader.addValidationError(SAMValidationError error) |
static void |
SAMUtils.processValidationError(SAMValidationError validationError,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
---|---|
static void |
SAMUtils.processValidationErrors(java.util.List<SAMValidationError> validationErrors,
long samRecordIndex,
ValidationStringency validationStringency)
Handle a list of validation errors according to the validation stringency.
|
void |
SAMFileHeader.setValidationErrors(java.util.Collection<SAMValidationError> errors)
Replace list of validation errors with the elements of the given list.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<SAMValidationError> |
SRALazyRecord.isValid(boolean firstOnly) |