Package htsjdk.samtools

Class SamReader.PrimitiveSamReaderToSamReaderAdapter

java.lang.Object

htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter

All Implemented Interfaces:

SamReader, SamReader.Indexing, Closeable, AutoCloseable, Iterable<SAMRecord>

Enclosing interface:

SamReader

public static class SamReader.PrimitiveSamReaderToSamReaderAdapter
extends Object
implements SamReader, SamReader.Indexing

Decorator for a 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.

Nested Class Summary

Nested classes/interfaces inherited from interface htsjdk.samtools.SamReader

SamReader.AssertingIterator, SamReader.Indexing, SamReader.PrimitiveSamReader, SamReader.PrimitiveSamReaderToSamReaderAdapter, SamReader.ReaderImplementation, SamReader.Type

Constructor Summary

Constructors

Constructor	Description
PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader p, SamInputResource resource)

Method Summary

Modifier and Type	Method	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.
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.
boolean	isQueryable()
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(String sequence, int start, int end, boolean contained)	Iterate over records that match the given interval.
SAMRecordIterator	queryAlignmentStart(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(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(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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

PrimitiveSamReaderToSamReaderAdapter

public PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader p,
 SamInputResource resource)

Method Details

underlyingReader

public SamReader.PrimitiveSamReader underlyingReader()

Access the underlying SamReader.PrimitiveSamReader used by this adapter.

Returns:

the SamReader.PrimitiveSamReader used by this adapter.

queryOverlapping

public SAMRecordIterator queryOverlapping(String sequence,
 int start,
 int end)

Description copied from interface: SamReader

Iterate over records that overlap the given interval. Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

queryOverlapping in interface SamReader

Parameters:

sequence - 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.

Returns:

Iterator over the SAMRecords overlapping the interval.

queryOverlapping

public SAMRecordIterator queryOverlapping(QueryInterval[] intervals)

Description copied from interface: SamReader

Iterate over records that overlap any of the given intervals. This may be more efficient than querying each interval separately, because multiple reads of the same SAMRecords is avoided.

Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

queryOverlapping in interface SamReader

Parameters:

intervals - 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[])

queryContained

public SAMRecordIterator queryContained(String sequence,
 int start,
 int end)

Description copied from interface: SamReader

Iterate over records that are contained in the given interval. Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

queryContained in interface SamReader

Parameters:

sequence - 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.

Returns:

Iterator over the SAMRecords contained in the interval.

queryContained

public SAMRecordIterator queryContained(QueryInterval[] intervals)

Description copied from interface: SamReader

Iterate over records that are contained in the given interval. This may be more efficient than querying each interval separately, because multiple reads of the same SAMRecords is avoided.

Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

queryContained in interface SamReader

Parameters:

intervals - 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[])

Returns:

Iterator over the SAMRecords contained in any of the intervals.

queryMate

public SAMRecord queryMate(SAMRecord rec)

Wraps the boilerplate code for querying a record's mate, which is common across many implementations.

Specified by:

queryMate in interface SamReader

Parameters:

rec - Record for which mate is sought. Must be a paired read.

Returns:

hasBrowseableIndex

public boolean hasBrowseableIndex()

Description copied from interface: SamReader.Indexing

Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.

Specified by:

hasBrowseableIndex in interface SamReader.Indexing

Returns:

True if the index supports the BrowseableBAMIndex interface. False otherwise.

getBrowseableIndex

public BrowseableBAMIndex getBrowseableIndex()

Description copied from interface: SamReader.Indexing

Gets an index tagged with the BrowseableBAMIndex interface. Throws an exception if no such index is available.

Specified by:

getBrowseableIndex in interface SamReader.Indexing

Returns:

An index with a browseable interface, if possible.

iterator

public SAMRecordIterator iterator()

Description copied from interface: SamReader

Iterate through file in order. For a SamReader constructed from an InputStream, and for any SAM file, a 2nd iteration starts where the 1st one left off. For a BAM constructed from a SeekableStream or File, each new iteration starts at the first record.

Only a single open iterator on a SAM or BAM file may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Specified by:

iterator in interface Iterable<SAMRecord>

Specified by:

iterator in interface SamReader

iterator

public SAMRecordIterator iterator(SAMFileSpan chunks)

Description copied from interface: SamReader.Indexing

Iterate through the given chunks in the file.

Specified by:

iterator in interface SamReader.Indexing

Parameters:

chunks - List of chunks for which to retrieve data.

Returns:

An iterator over the given chunks.

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

getFilePointerSpanningReads

public SAMFileSpan getFilePointerSpanningReads()

Description copied from interface: SamReader.Indexing

Gets a pointer spanning all reads in the BAM file.

Specified by:

getFilePointerSpanningReads in interface SamReader.Indexing

Returns:

Unbounded pointer to the first record, in chunk format.

getFileHeader

public SAMFileHeader getFileHeader()

Specified by:

getFileHeader in interface SamReader

type

public SamReader.Type type()

Specified by:

type in interface SamReader

Returns:

the SamReader.Type of this SamReader

getResourceDescription

public String getResourceDescription()

Specified by:

getResourceDescription in interface SamReader

Returns:

a human readable description of the resource backing this sam reader

isQueryable

public boolean isQueryable()

Specified by:

isQueryable in interface SamReader

Returns:

true if this source can be queried by interval, regardless of whether it has an index

hasIndex

public boolean hasIndex()

Specified by:

hasIndex in interface SamReader

Returns:

true if ths is a BAM file, and has an index

indexing

public SamReader.Indexing indexing()

Description copied from interface: SamReader

Exposes the SamReader.Indexing facet of this SamReader.

Specified by:

indexing in interface SamReader

getIndex

public BAMIndex getIndex()

Description copied from interface: SamReader.Indexing

Retrieves the index for the given file type. Ensure that the index is of the specified type.

Specified by:

getIndex in interface SamReader.Indexing

Returns:

An index of the given type.

query

public SAMRecordIterator query(QueryInterval[] intervals,
 boolean contained)

Description copied from interface: SamReader

Iterate over records that match one of the given intervals. This may be more efficient than querying each interval separately, because multiple reads of the same SAMRecords is avoided.

Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first. You can use a second SamReader to iterate in parallel over the same underlying file.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match an interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

query in interface SamReader

Parameters:

intervals - 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.

Returns:

Iterator over the SAMRecords matching the interval.

query

public SAMRecordIterator query(String sequence,
 int start,
 int end,
 boolean contained)

Description copied from interface: SamReader

Iterate over records that match the given interval. Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first. You can use a second SamReader to iterate in parallel over the same underlying file.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region.

Specified by:

query in interface SamReader

Parameters:

sequence - 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.

Returns:

Iterator over the SAMRecords matching the interval.

queryUnmapped

public SAMRecordIterator queryUnmapped()

Specified by:

queryUnmapped in interface SamReader

queryAlignmentStart

public SAMRecordIterator queryAlignmentStart(String sequence,
 int start)

Description copied from interface: SamReader

Iterate over records that map to the given sequence and start at the given position. Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SamReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that matches the arguments.

Specified by:

queryAlignmentStart in interface SamReader

Parameters:

sequence - Reference sequence of interest.

start - Alignment start of interest.

Returns:

Iterator over the SAMRecords with the given alignment start.