Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.digest | |
htsjdk.samtools.cram.structure | |
htsjdk.samtools.sra |
Modifier and Type | Class and Description |
---|---|
class |
SAMBinaryTagAndUnsignedArrayValue
Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because
signedness cannot be determined by introspection of value.
|
Modifier and Type | Field and Description |
---|---|
protected SAMBinaryTagAndValue |
SAMBinaryTagAndValue.next |
Modifier and Type | Method and Description |
---|---|
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.copy()
Creates and returns a shallow copy of the list of tag/values.
|
SAMBinaryTagAndValue |
SAMBinaryTagAndUnsignedArrayValue.copy()
Creates and returns a shallow copy of the list of tag/values.
|
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.deepCopy()
Creates and returns a deep copy of the list of tag/values.
|
SAMBinaryTagAndValue |
SAMBinaryTagAndUnsignedArrayValue.deepCopy()
Creates and returns a deep copy of the list of tag/values.
|
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.find(short tag)
Returns the SAMBinaryTagAndValue that contains the required tag, or null if not contained.
|
protected SAMBinaryTagAndValue |
BAMRecord.getBinaryAttributes() |
protected SAMBinaryTagAndValue |
SAMRecord.getBinaryAttributes() |
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.getNext() |
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue attr)
Inserts at item into the ordered list of attributes and returns the head of the list/sub-list
|
static SAMBinaryTagAndValue |
BinaryTagCodec.readTags(byte[] binaryRep,
int offset,
int length,
ValidationStringency validationStringency)
Convert tags from little-endian disk representation to in-memory representation.
|
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.remove(short tag)
Removes a tag from the list and returns the new head of the list/sub-list.
|
Modifier and Type | Method and Description |
---|---|
SAMBinaryTagAndValue |
SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue attr)
Inserts at item into the ordered list of attributes and returns the head of the list/sub-list
|
protected void |
SAMRecord.setAttributes(SAMBinaryTagAndValue attributes)
Replace any existing attributes with the given linked item.
|
Modifier and Type | Method and Description |
---|---|
SAMBinaryTagAndValue |
ContentDigests.getAsTags() |
Modifier and Type | Method and Description |
---|---|
static ContentDigests |
ContentDigests.create(SAMBinaryTagAndValue binaryTags) |
boolean |
ContentDigests.test(SAMBinaryTagAndValue tags) |
Modifier and Type | Field and Description |
---|---|
SAMBinaryTagAndValue |
Slice.sliceTags |
Modifier and Type | Method and Description |
---|---|
protected SAMBinaryTagAndValue |
SRALazyRecord.getBinaryAttributes() |
Modifier and Type | Method and Description |
---|---|
protected void |
SRALazyRecord.setAttributes(SAMBinaryTagAndValue attributes) |