Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.ref | |
htsjdk.samtools.reference | |
htsjdk.samtools.sra |
Modifier and Type | Method and Description |
---|---|
boolean |
SamFileValidator.validateSamFileSummary(SamReader samReader,
ReferenceSequenceFile reference)
Outputs validation summary report to out.
|
boolean |
SamFileValidator.validateSamFileVerbose(SamReader samReader,
ReferenceSequenceFile reference)
Outputs validation error details to out.
|
Constructor and Description |
---|
ReferenceSource(ReferenceSequenceFile rsFile) |
Modifier and Type | Class and Description |
---|---|
class |
FastaSequenceFile
Implementation of ReferenceSequenceFile for reading from FASTA files.
|
class |
IndexedFastaSequenceFile
A fasta file driven by an index for fast, concurrent lookups.
|
Modifier and Type | Method and Description |
---|---|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file,
boolean truncateNamesAtWhitespace)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file,
boolean truncateNamesAtWhitespace,
boolean preferIndexed)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path,
boolean truncateNamesAtWhitespace)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
static ReferenceSequenceFile |
ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path,
boolean truncateNamesAtWhitespace,
boolean preferIndexed)
Attempts to determine the type of the reference file and return an instance
of ReferenceSequenceFile that is appropriate to read it.
|
Constructor and Description |
---|
ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile) |
Modifier and Type | Class and Description |
---|---|
class |
SRAIndexedSequenceFile
Allows reading Reference data from SRA
|