htsjdk.tribble.readers

Class TabixReader

java.lang.Object

htsjdk.tribble.readers.TabixReader

public class TabixReader
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	TabixReader.Iterator
protected static class	TabixReader.TIndex
protected static class	TabixReader.TPair64

Field Summary

Fields

Modifier and Type	Field and Description
protected TabixReader.TIndex[]	mIndex

Constructor Summary

Constructors

Constructor and Description
TabixReader(java.lang.String filePath)
TabixReader(java.lang.String filePath, SeekableStream stream)
TabixReader(java.lang.String filePath, java.lang.String indexPath)
TabixReader(java.lang.String filePath, java.lang.String indexPath, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)
TabixReader(java.lang.String filePath, java.lang.String indexPath, SeekableStream stream)
TabixReader(java.lang.String filePath, java.lang.String indexPath, SeekableStream stream, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)

Method Summary

Modifier and Type	Method and Description
int	chr2tid(java.lang.String chr) return chromosome ID or -1 if it is unknown
void	close()
java.util.Set<java.lang.String>	getChromosomes() return the chromosomes in that tabix file
java.lang.String	getSource() return the source (filename/URL) of that reader
int[]	parseReg(java.lang.String reg) Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
TabixReader.Iterator	query(int tid, int beg, int end) Return
TabixReader.Iterator	query(java.lang.String reg)
TabixReader.Iterator	query(java.lang.String reg, int start, int end)
static int	readInt(java.io.InputStream is)
java.lang.String	readLine() Read one line from the data file.
static java.lang.String	readLine(java.io.InputStream is)
static long	readLong(java.io.InputStream is)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

mIndex

protected TabixReader.TIndex[] mIndex

Constructor Detail

TabixReader

public TabixReader(java.lang.String filePath)
            throws java.io.IOException

Parameters:

filePath - path to the data file/uri

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String filePath,
                   java.lang.String indexPath)
            throws java.io.IOException

Parameters:

filePath - path to the of the data file/uri

indexPath - Full path to the index file. Auto-generated if null

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String filePath,
                   java.lang.String indexPath,
                   java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper,
                   java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)
            throws java.io.IOException

Parameters:

filePath - path to the data file/uri

indexPath - Full path to the index file. Auto-generated if null

wrapper - a wrapper to apply to the raw byte stream of the data file if is a uri representing a Path

indexWrapper - a wrapper to apply to the raw byte stream of the index file if it is a uri representing a Path

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String filePath,
                   SeekableStream stream)
            throws java.io.IOException

Parameters:

filePath - Path to the data file (used for error messages only)

stream - Seekable stream from which the data is read

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String filePath,
                   java.lang.String indexPath,
                   SeekableStream stream)
            throws java.io.IOException

Parameters:

filePath - Path to the data file (used for error messages only)

indexPath - Full path to the index file. Auto-generated if null

stream - Seekable stream from which the data is read

Throws:

java.io.IOException

TabixReader

public TabixReader(java.lang.String filePath,
                   java.lang.String indexPath,
                   SeekableStream stream,
                   java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)
            throws java.io.IOException

Parameters:

filePath - Path to the data file (used for error messages only)

indexPath - Full path to the index file. Auto-generated if null

indexWrapper - a wrapper to apply to the raw byte stream of the index file if it is a uri representing a Path

stream - Seekable stream from which the data is read

Throws:

java.io.IOException

Method Detail

getSource

public java.lang.String getSource()

return the source (filename/URL) of that reader

readInt

public static int readInt(java.io.InputStream is)
                   throws java.io.IOException

Throws:

java.io.IOException

readLong

public static long readLong(java.io.InputStream is)
                     throws java.io.IOException

Throws:

java.io.IOException

readLine

public static java.lang.String readLine(java.io.InputStream is)
                                 throws java.io.IOException

Throws:

java.io.IOException

readLine

public java.lang.String readLine()
                          throws java.io.IOException

Read one line from the data file.

Throws:

java.io.IOException

chr2tid

public int chr2tid(java.lang.String chr)

return chromosome ID or -1 if it is unknown

getChromosomes

public java.util.Set<java.lang.String> getChromosomes()

return the chromosomes in that tabix file

parseReg

public int[] parseReg(java.lang.String reg)

Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"

Parameters:

reg - Region string

Returns:

An array where the three elements are sequence_id, region_begin and region_end. On failure, sequence_id==-1.

query

public TabixReader.Iterator query(int tid,
                                  int beg,
                                  int end)

Return

Parameters:

tid - Sequence id

beg - beginning of interval, genomic coords

end - end of interval, genomic coords

Returns:

an iterator over the lines within the specified interval

query

public TabixReader.Iterator query(java.lang.String reg)

Parameters:

reg - A region string of the form acceptable by parseReg(String)

Returns:

See Also:

parseReg(String)

query

public TabixReader.Iterator query(java.lang.String reg,
                                  int start,
                                  int end)

Parameters:

reg - a chromosome

start - start interval

end - end interval

Returns:

a tabix iterator

See Also:

parseReg(String)

close

public void close()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object