Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.ref | |
htsjdk.samtools.util | |
htsjdk.variant.vcf |
Modifier and Type | Method and Description |
---|---|
SAMSequenceRecord |
SAMSequenceDictionary.addSequenceAlias(java.lang.String originalName,
java.lang.String altName)
Add an alias to a SAMSequenceRecord.
|
SAMSequenceRecord |
SAMSequenceRecord.clone() |
SAMSequenceRecord |
SAMFileHeader.getSequence(int sequenceIndex)
Look up a sequence record by index.
|
SAMSequenceRecord |
SAMSequenceDictionary.getSequence(int sequenceIndex) |
SAMSequenceRecord |
SAMFileHeader.getSequence(java.lang.String name)
Look up sequence record by name.
|
SAMSequenceRecord |
SAMSequenceDictionary.getSequence(java.lang.String name) |
Modifier and Type | Method and Description |
---|---|
java.util.List<SAMSequenceRecord> |
SAMSequenceDictionary.getSequences() |
Modifier and Type | Method and Description |
---|---|
void |
SAMFileHeader.addSequence(SAMSequenceRecord sequenceRecord) |
void |
SAMSequenceDictionary.addSequence(SAMSequenceRecord sequenceRecord) |
boolean |
SAMSequenceRecord.isSameSequence(SAMSequenceRecord that)
Looser comparison than equals().
|
Modifier and Type | Method and Description |
---|---|
void |
SAMSequenceDictionary.setSequences(java.util.List<SAMSequenceRecord> list)
Replaces the existing list of SAMSequenceRecords with the given list.
|
Constructor and Description |
---|
SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list) |
Modifier and Type | Method and Description |
---|---|
byte[] |
ReferenceSource.getReferenceBases(SAMSequenceRecord record,
boolean tryNameVariants) |
Modifier and Type | Method and Description |
---|---|
static void |
SequenceUtil.assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
java.util.List<SAMSequenceRecord> s2)
default signature that forces the lists to be the same size
|
static void |
SequenceUtil.assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
java.util.List<SAMSequenceRecord> s2)
default signature that forces the lists to be the same size
|
static void |
SequenceUtil.assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
java.util.List<SAMSequenceRecord> s2,
boolean checkPrefixOnly)
Throws an exception only if both (first) parameters are not null
optionally check that one list is a (nonempty) prefix of the other.
|
static void |
SequenceUtil.assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
java.util.List<SAMSequenceRecord> s2,
boolean checkPrefixOnly)
Throws an exception only if both (first) parameters are not null
optionally check that one list is a (nonempty) prefix of the other.
|
Modifier and Type | Method and Description |
---|---|
SAMSequenceRecord |
VCFContigHeaderLine.getSAMSequenceRecord() |