htsjdk.tribble.index.tabix

Class TabixIndex

java.lang.Object

htsjdk.tribble.index.tabix.TabixIndex

All Implemented Interfaces:

Index

public class TabixIndex
extends java.lang.Object
implements Index

This class represent a Tabix index that has been built in memory or read from a file. It can be queried or written to a file.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAGIC_NUMBER

Constructor Summary

Constructors

Constructor and Description
TabixIndex(java.io.File tabixFile) Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.
TabixIndex(java.io.InputStream inputStream)
TabixIndex(TabixFormat formatSpec, java.util.List<java.lang.String> sequenceNames, BinningIndexContent[] indices)

Method Summary

Modifier and Type	Method and Description
boolean	containsChromosome(java.lang.String chr)
boolean	equals(java.lang.Object o)
boolean	equalsIgnoreProperties(java.lang.Object o) Returns true if this and obj are 'effectively' equivalent indices.
java.util.List<Block>	getBlocks(java.lang.String chr, int start, int end) Query the index.
TabixFormat	getFormatSpec()
java.util.Map<java.lang.String,java.lang.String>	getProperties() No arbitrary properties in Tabix
java.util.List<java.lang.String>	getSequenceNames()
int	hashCode()
boolean	isCurrentVersion()
void	write(java.io.File tabixFile) Writes the index with BGZF.
void	write(LittleEndianOutputStream los) all indexes are writable to disk
void	writeBasedOnFeatureFile(java.io.File featureFile) Writes to a file with appropriate name and directory based on feature file.

Methods inherited from class java.lang.Object

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

Field Detail

MAGIC_NUMBER

public static final int MAGIC_NUMBER

Constructor Detail

TabixIndex

public TabixIndex(TabixFormat formatSpec,
                  java.util.List<java.lang.String> sequenceNames,
                  BinningIndexContent[] indices)

Parameters:

formatSpec - Information about how to interpret the file being indexed. Unused by this class other than written to an output file.

sequenceNames - Sequences in the file being indexed, in the order they appear in the file.

indices - One for each element of sequenceNames

TabixIndex

public TabixIndex(java.io.InputStream inputStream)
           throws java.io.IOException

Parameters:

inputStream - This is expected to be buffered and be gzip-decompressing as appropriate. Caller should close input stream after ctor returns.

Throws:

java.io.IOException

TabixIndex

public TabixIndex(java.io.File tabixFile)
           throws java.io.IOException

Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.

Throws:

java.io.IOException

Method Detail

getBlocks

public java.util.List<Block> getBlocks(java.lang.String chr,
                                       int start,
                                       int end)

Description copied from interface: Index

Query the index.

Specified by:

getBlocks in interface Index

Parameters:

chr - the chromosome

start - the start position, one-based, inclusive.

end - the end position, one-based, inclusive.

Returns:

List of regions of file that are candidates for the given query.

TODO: This method has not yet been tested, since the primary task is index writing.

isCurrentVersion

public boolean isCurrentVersion()

Specified by:

isCurrentVersion in interface Index

Returns:

true if the index is up to date, false otherwise

getSequenceNames

public java.util.List<java.lang.String> getSequenceNames()

Specified by:

getSequenceNames in interface Index

Returns:

a list of the sequence names we've seen during indexing, in order

containsChromosome

public boolean containsChromosome(java.lang.String chr)

Specified by:

containsChromosome in interface Index

Parameters:

chr - the chromosome (or contig) name

Returns:

true if we have an entry; false otherwise

getProperties

public java.util.Map<java.lang.String,java.lang.String> getProperties()

No arbitrary properties in Tabix

Specified by:

getProperties in interface Index

Returns:

get the list of properties for this index. Returns null if no properties.

equalsIgnoreProperties

public boolean equalsIgnoreProperties(java.lang.Object o)

Description copied from interface: Index

Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices

Specified by:

equalsIgnoreProperties in interface Index

Returns:

getFormatSpec

public TabixFormat getFormatSpec()

write

public void write(java.io.File tabixFile)
           throws java.io.IOException

Writes the index with BGZF.

Specified by:

write in interface Index

Parameters:

tabixFile - Where to write the index.

Throws:

java.io.IOException - if the index is unable to write to the specified file

writeBasedOnFeatureFile

public void writeBasedOnFeatureFile(java.io.File featureFile)
                             throws java.io.IOException

Writes to a file with appropriate name and directory based on feature file.

Specified by:

writeBasedOnFeatureFile in interface Index

Parameters:

featureFile - File being indexed.

Throws:

java.io.IOException

write

public void write(LittleEndianOutputStream los)
           throws java.io.IOException

Description copied from interface: Index

all indexes are writable to disk

Specified by:

write in interface Index

Parameters:

los - It is assumes that caller has done appropriate buffering and BlockCompressedOutputStream wrapping. Caller should close output stream after invoking this method.

Throws:

java.io.IOException

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object