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

All Methods Instance Methods Concrete Methods
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`.
`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 Detail
  - PrimitiveSamReaderToSamReaderAdapter
```
public PrimitiveSamReaderToSamReaderAdapter(SamReader.PrimitiveSamReader p,
                                            SamInputResource resource)
```
- Method Detail
  - 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
  - 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.

Class SamReader.PrimitiveSamReaderToSamReaderAdapter

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

PrimitiveSamReaderToSamReaderAdapter

Method Detail

underlyingReader

queryOverlapping

queryOverlapping

queryContained

queryContained

queryMate

hasBrowseableIndex

getBrowseableIndex

iterator

iterator

close

getFilePointerSpanningReads

getFileHeader

type

getResourceDescription

hasIndex

indexing

getIndex

query

query

queryUnmapped

queryAlignmentStart