Package | Description |
---|---|
htsjdk.samtools.reference | |
htsjdk.samtools.sra |
Modifier and Type | Method and Description |
---|---|
ReferenceSequence |
ReferenceSequenceFileWalker.get(int sequenceIndex)
Get reference sequence without validating name or length.
|
ReferenceSequence |
ReferenceSequenceFileWalker.get(int sequenceIndex,
java.lang.String sequenceName,
int length)
Ensure that the requested sequence is loaded.
|
ReferenceSequence |
ReferenceSequenceFile.getSequence(java.lang.String contig)
Retrieves the complete sequence described by this contig.
|
ReferenceSequence |
IndexedFastaSequenceFile.getSequence(java.lang.String contig)
Retrieves the complete sequence described by this contig.
|
ReferenceSequence |
ReferenceSequenceFile.getSubsequenceAt(java.lang.String contig,
long start,
long stop)
Gets the subsequence of the contig in the range [start,stop]
|
ReferenceSequence |
IndexedFastaSequenceFile.getSubsequenceAt(java.lang.String contig,
long start,
long stop)
Gets the subsequence of the contig in the range [start,stop]
|
ReferenceSequence |
ReferenceSequenceFile.nextSequence()
Retrieves the next whole sequences from the file.
|
ReferenceSequence |
FastaSequenceFile.nextSequence() |
ReferenceSequence |
IndexedFastaSequenceFile.nextSequence()
Gets the next sequence if available, or null if not present.
|
Modifier and Type | Method and Description |
---|---|
ReferenceSequence |
SRAIndexedSequenceFile.getSequence(java.lang.String contig) |
ReferenceSequence |
SRAIndexedSequenceFile.getSubsequenceAt(java.lang.String contig,
long start,
long stop) |
ReferenceSequence |
SRAIndexedSequenceFile.nextSequence() |