Modifier and Type | Method and Description |
---|---|
SAMSequenceDictionary |
SAMFileHeader.getSequenceDictionary() |
static SAMSequenceDictionary |
SAMFileReader.getSequenceDictionary(java.io.File dictionaryFile)
Deprecated.
Returns the SAMSequenceDictionary from the provided FASTA.
|
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
SamIndexes.asBaiSeekableStreamOrNull(SeekableStream inputStream,
SAMSequenceDictionary dictionary) |
static java.io.InputStream |
SamIndexes.asBaiStreamOrNull(java.io.InputStream inputStream,
SAMSequenceDictionary dictionary) |
void |
SAMSequenceDictionary.assertSameDictionary(SAMSequenceDictionary that)
Non-comprehensive
equals(Object) -assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent
SAMSequenceRecord s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord) . |
static java.io.InputStream |
SamIndexes.openIndexFileAsBaiOrNull(java.io.File file,
SAMSequenceDictionary dictionary) |
static java.io.InputStream |
SamIndexes.openIndexUrlAsBaiOrNull(java.net.URL url,
SAMSequenceDictionary dictionary) |
void |
SAMFileHeader.setSequenceDictionary(SAMSequenceDictionary sequenceDictionary)
Replace entire sequence dictionary.
|
Constructor and Description |
---|
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary) |
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary,
boolean useMemoryMapping) |
AbstractBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
CRAIIndex.openCraiFileAsBaiStream(java.io.File cramIndexFile,
SAMSequenceDictionary dictionary) |
static SeekableStream |
CRAIIndex.openCraiFileAsBaiStream(java.io.InputStream indexStream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
void |
LiftOver.validateToSequences(SAMSequenceDictionary sequenceDictionary)
Throw an exception if all the "to" sequence names in the chains are not found in the given sequence dictionary.
|
Modifier and Type | Method and Description |
---|---|
SAMSequenceDictionary |
IndexedFastaSequenceFile.getSequenceDictionary()
Retrieves the sequence dictionary for the fasta file.
|
SAMSequenceDictionary |
ReferenceSequenceFile.getSequenceDictionary()
Must return a sequence dictionary with at least the following fields completed
for each sequence: name, length.
|
SAMSequenceDictionary |
ReferenceSequenceFileWalker.getSequenceDictionary() |
Modifier and Type | Method and Description |
---|---|
protected static void |
IndexedFastaSequenceFile.sanityCheckDictionaryAgainstIndex(java.lang.String fastaFile,
SAMSequenceDictionary sequenceDictionary,
FastaSequenceIndex index)
Do some basic checking to make sure the dictionary and the index match.
|
Modifier and Type | Field and Description |
---|---|
protected SAMSequenceDictionary |
SRAIndexedSequenceFile.sequenceDictionary |
Modifier and Type | Method and Description |
---|---|
SAMSequenceDictionary |
SRAIndexedSequenceFile.getSequenceDictionary() |
protected SAMSequenceDictionary |
SRAIndexedSequenceFile.loadSequenceDictionary() |
Modifier and Type | Method and Description |
---|---|
static boolean |
SequenceUtil.areSequenceDictionariesEqual(SAMSequenceDictionary s1,
SAMSequenceDictionary s2)
Returns true if both parameters are null or equal, otherwise returns false
|
static void |
IntervalUtil.assertOrderedNonOverlapping(java.util.Iterator<Interval> intervals,
SAMSequenceDictionary sequenceDictionary)
Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
|
static void |
SequenceUtil.assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
SAMSequenceDictionary s2)
Throws an exception if both parameters are non-null and unequal.
|
static void |
SequenceUtil.assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
SAMSequenceDictionary s2,
boolean checkPrefixOnly)
Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only).
|
static void |
SequenceUtil.assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
SAMSequenceDictionary s2,
java.io.File f1,
java.io.File f2)
Throws an exception if both parameters are non-null and unequal, including the filenames.
|
Modifier and Type | Method and Description |
---|---|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.createTabixIndex(java.io.File inputFile,
FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
TabixFormat tabixFormat,
SAMSequenceDictionary sequenceDictionary) |
Constructor and Description |
---|
TabixIndexCreator(SAMSequenceDictionary sequenceDictionary,
TabixFormat formatSpec) |
Modifier and Type | Method and Description |
---|---|
static SAMSequenceDictionary |
TabixUtils.getSequenceDictionary(java.io.File tabixIndex)
Generates the SAMSequenceDictionary from the given tabix index file
|
Modifier and Type | Method and Description |
---|---|
static SAMSequenceDictionary |
SAMSequenceDictionaryExtractor.extractDictionary(java.io.File file) |
Modifier and Type | Method and Description |
---|---|
static java.util.List<java.lang.String> |
VariantContextComparator.getSequenceNameList(SAMSequenceDictionary dictionary) |
Constructor and Description |
---|
VariantContextComparator(SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
SAMSequenceDictionary refDict)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBcf2(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBcf2(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBlockCompressedVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBlockCompressedVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
VariantContextWriterBuilder |
VariantContextWriterBuilder.setReferenceDictionary(SAMSequenceDictionary refDict)
Set the reference dictionary to be used by
VariantContextWriter s created by this builder. |
Modifier and Type | Method and Description |
---|---|
SAMSequenceDictionary |
VCFHeader.getSequenceDictionary()
Returns the contigs in this VCF file as a SAMSequenceDictionary.
|
static SAMSequenceDictionary |
VCFFileReader.getSequenceDictionary(java.io.File file)
Returns the SAMSequenceDictionary from the provided VCF file.
|
Modifier and Type | Method and Description |
---|---|
static java.util.List<VCFContigHeaderLine> |
VCFUtils.makeContigHeaderLines(SAMSequenceDictionary refDict,
java.io.File referenceFile)
Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null
|
void |
VCFHeader.setSequenceDictionary(SAMSequenceDictionary dictionary)
Completely replaces the contig records in this header with those in the given SAMSequenceDictionary.
|
static VCFHeader |
VCFUtils.withUpdatedContigs(VCFHeader oldHeader,
java.io.File referenceFile,
SAMSequenceDictionary refDict)
Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
|
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict) |
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict,
boolean referenceNameOnly) |