Package htsjdk.tribble.index.tabix
Class TabixIndex
java.lang.Object
htsjdk.tribble.index.tabix.TabixIndex
- All Implemented Interfaces:
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.
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Field Summary
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Constructor Summary
ConstructorDescriptionTabixIndex
(TabixFormat formatSpec, List<String> sequenceNames, BinningIndexContent[] indices) TabixIndex
(File tabixFile) Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.TabixIndex
(InputStream inputStream) TabixIndex
(Path tabixPath) Convenient ctor that opens the path, wraps with with BGZF reader, and closes after reading index. -
Method Summary
Modifier and TypeMethodDescriptionboolean
containsChromosome
(String chr) boolean
boolean
Returns true if this and obj are 'effectively' equivalent indices.Query the index.No arbitrary properties in Tabixint
hashCode()
boolean
void
all indexes are writable to diskvoid
Writes the index with BGZF.void
writeBasedOnFeaturePath
(Path featurePath) Writes to a path with appropriate name and directory based on feature path.Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.tribble.index.Index
write, writeBasedOnFeatureFile
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Field Details
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MAGIC_NUMBER
public static final int MAGIC_NUMBER
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Constructor Details
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TabixIndex
public TabixIndex(TabixFormat formatSpec, List<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
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TabixIndex
- Parameters:
inputStream
- This is expected to be buffered and be gzip-decompressing as appropriate. Caller should close input stream after ctor returns.- Throws:
IOException
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TabixIndex
Convenient ctor that opens the file, wraps with with BGZF reader, and closes after reading index.- Throws:
IOException
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TabixIndex
Convenient ctor that opens the path, wraps with with BGZF reader, and closes after reading index.- Throws:
IOException
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Method Details
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getBlocks
Description copied from interface:Index
Query the index.- Specified by:
getBlocks
in interfaceIndex
- Parameters:
chr
- the chromosomestart
- 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.
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isCurrentVersion
public boolean isCurrentVersion()- Specified by:
isCurrentVersion
in interfaceIndex
- Returns:
- true if the index is up to date, false otherwise
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getSequenceNames
- Specified by:
getSequenceNames
in interfaceIndex
- Returns:
- a list of the sequence names we've seen during indexing, in order
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containsChromosome
- Specified by:
containsChromosome
in interfaceIndex
- Parameters:
chr
- the chromosome (or contig) name- Returns:
- true if we have an entry; false otherwise
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getProperties
No arbitrary properties in Tabix- Specified by:
getProperties
in interfaceIndex
- Returns:
- get the list of properties for this index. Returns null if no properties.
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equalsIgnoreProperties
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 interfaceIndex
- Returns:
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getFormatSpec
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getIndices
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write
Writes the index with BGZF.- Specified by:
write
in interfaceIndex
- Parameters:
tabixPath
- Where to write the index.- Throws:
IOException
- if the index is unable to write to the specified path.
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writeBasedOnFeaturePath
Writes to a path with appropriate name and directory based on feature path.- Specified by:
writeBasedOnFeaturePath
in interfaceIndex
- Parameters:
featurePath
- Path being indexed.- Throws:
IOException
- if featureFile is not a normal file.
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write
Description copied from interface:Index
all indexes are writable to disk- Specified by:
write
in interfaceIndex
- Parameters:
los
- It is assumes that caller has done appropriate buffering and BlockCompressedOutputStream wrapping. Caller should close output stream after invoking this method.- Throws:
IOException
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equals
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hashCode
public int hashCode()
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