java.lang.Object
- htsjdk.samtools.SamReader.ReaderImplementation
- - htsjdk.samtools.SRAFileReader

All Implemented Interfaces:: SamReader.Indexing, SamReader.PrimitiveSamReader

public class SRAFileReader
extends SamReader.ReaderImplementation
implements SamReader.Indexing

Constructor Summary

Constructors
Constructor Description

SRAFileReader(SRAAccession acc)

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.
`CloseableIterator<SAMRecord>`	`getIterator()`
`CloseableIterator<SAMRecord>`	`getIterator(SAMFileSpan chunks)`
`protected SRAIterator.RecordRangeInfo`	`getRecordsRangeInfo()`
`ValidationStringency`	`getValidationStringency()`
`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()`
`SAMRecordIterator`	`iterator(SAMFileSpan chunks)`	Iterate through the given chunks in the file.
`CloseableIterator<SAMRecord>`	`query(QueryInterval[] intervals, boolean contained)`
`CloseableIterator<SAMRecord>`	`queryAlignmentStart(String sequence, int start)`
`CloseableIterator<SAMRecord>`	`queryUnmapped()`
`SamReader.Type`	`type()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.SamReader.PrimitiveSamReader
isQueryable

- Constructor Detail
  - SRAFileReader
```
public SRAFileReader(SRAAccession acc)
```
- Method Detail
  - type
```
public SamReader.Type type()
```
    Specified by:
    
    type in interface SamReader.PrimitiveSamReader
  - hasIndex
```
public boolean hasIndex()
```
    Specified by:
    
    hasIndex in interface SamReader.PrimitiveSamReader
  - 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
    
    Specified by:
    
    getIndex in interface SamReader.PrimitiveSamReader
    
    Returns:
    
    An index of the given type.
  - getFileHeader
```
public SAMFileHeader getFileHeader()
```
    Specified by:
    
    getFileHeader in interface SamReader.PrimitiveSamReader
  - getIterator
```
public CloseableIterator<SAMRecord> getIterator()
```
    Specified by:
    
    getIterator in interface SamReader.PrimitiveSamReader
  - getIterator
```
public CloseableIterator<SAMRecord> getIterator(SAMFileSpan chunks)
```
    Specified by:
    
    getIterator in interface SamReader.PrimitiveSamReader
  - 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
    
    Specified by:
    
    getFilePointerSpanningReads in interface SamReader.PrimitiveSamReader
    
    Returns:
    
    Unbounded pointer to the first record, in chunk format.
  - query
```
public CloseableIterator<SAMRecord> query(QueryInterval[] intervals,
                                          boolean contained)
```
    Specified by:
    
    query in interface SamReader.PrimitiveSamReader
  - queryAlignmentStart
```
public CloseableIterator<SAMRecord> queryAlignmentStart(String sequence,
                                                        int start)
```
    Specified by:
    
    queryAlignmentStart in interface SamReader.PrimitiveSamReader
  - queryUnmapped
```
public CloseableIterator<SAMRecord> queryUnmapped()
```
    Specified by:
    
    queryUnmapped in interface SamReader.PrimitiveSamReader
  - close
```
public void close()
```
    Specified by:
    
    close in interface SamReader.PrimitiveSamReader
  - getValidationStringency
```
public ValidationStringency getValidationStringency()
```
    Specified by:
    
    getValidationStringency in interface SamReader.PrimitiveSamReader
  - hasBrowseableIndex
```
public boolean hasBrowseableIndex()
```
    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()
```
    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.
    
    Throws:
    
    SAMException - if no such index is available.
  - iterator
```
public SAMRecordIterator iterator(SAMFileSpan chunks)
```
    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.
  - getRecordsRangeInfo
```
protected SRAIterator.RecordRangeInfo getRecordsRangeInfo()
```

Class SRAFileReader

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.SamReader.PrimitiveSamReader

Constructor Detail

SRAFileReader

Method Detail

type

hasIndex

getIndex

getFileHeader

getIterator

getIterator

getFilePointerSpanningReads

query

queryAlignmentStart

queryUnmapped

close

getValidationStringency

hasBrowseableIndex

getBrowseableIndex

iterator

getRecordsRangeInfo