public static class SamReader.PrimitiveSamReaderToSamReaderAdapter extends java.lang.Object implements SamReader, SamReader.Indexing
SamReader.PrimitiveSamReader that expands its functionality into a SamReader,
given the backing SamInputResource.
Wraps the SamReader.Indexing interface as well, which was originally separate from SamReader but in practice
the two are always implemented by the same class.SamReader.AssertingIterator, SamReader.Indexing, SamReader.PrimitiveSamReader, SamReader.PrimitiveSamReaderToSamReaderAdapter, SamReader.ReaderImplementation, SamReader.Type| Constructor and Description |
|---|
PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader p,
SamInputResource resource) |
| Modifier and Type | Method and Description |
|---|---|
void |
close() |
BrowseableBAMIndex |
getBrowseableIndex()
Gets an index tagged with the BrowseableBAMIndex interface.
|
SAMFileHeader |
getFileHeader() |
SAMFileSpan |
getFilePointerSpanningReads()
Gets a pointer spanning all reads in the BAM file.
|
BAMIndex |
getIndex()
Retrieves the index for the given file type.
|
java.lang.String |
getResourceDescription() |
boolean |
hasBrowseableIndex()
Returns true if the supported index is browseable, meaning the bins in it can be traversed
and chunk data inspected and retrieved.
|
boolean |
hasIndex() |
SamReader.Indexing |
indexing()
Exposes the
SamReader.Indexing facet of this SamReader. |
SAMRecordIterator |
iterator()
Iterate through file in order.
|
SAMRecordIterator |
iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
SAMRecordIterator |
query(QueryInterval[] intervals,
boolean contained)
Iterate over records that match one of the given intervals.
|
SAMRecordIterator |
query(java.lang.String sequence,
int start,
int end,
boolean contained)
Iterate over records that match the given interval.
|
SAMRecordIterator |
queryAlignmentStart(java.lang.String sequence,
int start)
Iterate over records that map to the given sequence and start at the given position.
|
SAMRecordIterator |
queryContained(QueryInterval[] intervals)
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
queryContained(java.lang.String sequence,
int start,
int end)
Iterate over records that are contained in the given interval.
|
SAMRecord |
queryMate(SAMRecord rec)
Wraps the boilerplate code for querying a record's mate, which is common across many implementations.
|
SAMRecordIterator |
queryOverlapping(QueryInterval[] intervals)
Iterate over records that overlap any of the given intervals.
|
SAMRecordIterator |
queryOverlapping(java.lang.String sequence,
int start,
int end)
Iterate over records that overlap the given interval.
|
SAMRecordIterator |
queryUnmapped() |
SamReader.Type |
type() |
SamReader.PrimitiveSamReader |
underlyingReader()
Access the underlying
SamReader.PrimitiveSamReader used by this adapter. |
public PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader p, SamInputResource resource)
public SamReader.PrimitiveSamReader underlyingReader()
SamReader.PrimitiveSamReader used by this adapter.SamReader.PrimitiveSamReader used by this adapter.public SAMRecordIterator queryOverlapping(java.lang.String sequence, int start, int end)
SamReaderqueryOverlapping in interface SamReadersequence - Reference sequence of interest.start - 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end - 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.public SAMRecordIterator queryOverlapping(QueryInterval[] intervals)
SamReaderqueryOverlapping in interface SamReaderintervals - Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])public SAMRecordIterator queryContained(java.lang.String sequence, int start, int end)
SamReaderqueryContained in interface SamReadersequence - Reference sequence of interest.start - 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end - 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.public SAMRecordIterator queryContained(QueryInterval[] intervals)
SamReaderqueryContained in interface SamReaderintervals - Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])public SAMRecord queryMate(SAMRecord rec)
public boolean hasBrowseableIndex()
SamReader.IndexinghasBrowseableIndex in interface SamReader.Indexingpublic BrowseableBAMIndex getBrowseableIndex()
SamReader.IndexinggetBrowseableIndex in interface SamReader.Indexingpublic SAMRecordIterator iterator()
SamReaderpublic SAMRecordIterator iterator(SAMFileSpan chunks)
SamReader.Indexingiterator in interface SamReader.Indexingchunks - List of chunks for which to retrieve data.public void close()
close in interface java.io.Closeableclose in interface java.lang.AutoCloseablepublic SAMFileSpan getFilePointerSpanningReads()
SamReader.IndexinggetFilePointerSpanningReads in interface SamReader.Indexingpublic SAMFileHeader getFileHeader()
getFileHeader in interface SamReaderpublic SamReader.Type type()
type in interface SamReaderSamReader.Type of this SamReaderpublic java.lang.String getResourceDescription()
getResourceDescription in interface SamReaderpublic boolean hasIndex()
public SamReader.Indexing indexing()
SamReaderSamReader.Indexing facet of this SamReader.public BAMIndex getIndex()
SamReader.IndexinggetIndex in interface SamReader.Indexingpublic SAMRecordIterator query(QueryInterval[] intervals, boolean contained)
SamReaderquery in interface SamReaderintervals - Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])contained - If true, each SAMRecord returned is will have its alignment completely contained in one of the
intervals of interest. If false, the alignment of the returned SAMRecords need only overlap one of
the intervals of interest.public SAMRecordIterator query(java.lang.String sequence, int start, int end, boolean contained)
SamReaderquery in interface SamReadersequence - Reference sequence of interest.start - 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end - 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.contained - If true, each SAMRecord returned will have its alignment completely contained in the
interval of interest. If false, the alignment of the returned SAMRecords need only overlap the interval of interest.public SAMRecordIterator queryUnmapped()
queryUnmapped in interface SamReaderpublic SAMRecordIterator queryAlignmentStart(java.lang.String sequence, int start)
SamReaderqueryAlignmentStart in interface SamReadersequence - Reference sequence of interest.start - Alignment start of interest.