htsjdk.tribble.index.tabix

Class TabixIndexMerger

java.lang.Object

htsjdk.samtools.IndexMerger<TabixIndex>

htsjdk.tribble.index.tabix.TabixIndexMerger

public class TabixIndexMerger
extends IndexMerger<TabixIndex>

Merges tabix files for parts of a VCF file that have been concatenated. A partitioned VCF is a directory containing the following files:

1. A file named header containing all header bytes in VCF format.
2. Zero or more files named part-00000, part-00001, ... etc, containing a list of VCF records.
3. A file named terminator containing a BGZF end-of-file marker block (only if the VCF is bgzip-compressed).

If the VCF is bgzip-compressed then the header and part files must be all bgzip-compressed. For a compressed VCF, if an index is required, then a tabix index can be generated for each (headerless) part file. These files should be named .part-00000.tbi, .part-00001.tbi, ... etc. Note the leading . to make the files hidden. This format has the following properties:

• Parts and their indexes may be written in parallel, since one part file can be written independently of the others.
• A VCF file can be created from a partitioned VCF file by concatenating all the non-hidden files (header, part-00000, part-00001, ..., terminator).
• A VCF index can be created from a partitioned VCF file by merging all of the hidden files with a .tbi suffix. Note that this is not a simple file concatenation operation. See TabixIndexMerger.

Field Summary

Fields inherited from class htsjdk.samtools.IndexMerger

out, partLengths

Constructor Summary

Constructors

Constructor and Description
TabixIndexMerger(java.io.OutputStream out, long headerLength)

Method Summary

Modifier and Type	Method and Description
void	finish(long dataFileLength) Finish merging the indexes, and close the output stream.
void	processIndex(TabixIndex index, long partLength) Process the next index and add to the merged index.

Methods inherited from class java.lang.Object

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

Constructor Detail

TabixIndexMerger

public TabixIndexMerger(java.io.OutputStream out,
                        long headerLength)

Method Detail

processIndex

public void processIndex(TabixIndex index,
                         long partLength)

Description copied from class: IndexMerger

Process the next index and add to the merged index.

Specified by:

processIndex in class IndexMerger<TabixIndex>

Parameters:

index - the index to merge

partLength - the length of the part file corresponding to the index, in bytes.

finish

public void finish(long dataFileLength)
            throws java.io.IOException

Description copied from class: IndexMerger

Finish merging the indexes, and close the output stream.

Specified by:

finish in class IndexMerger<TabixIndex>

Parameters:

dataFileLength - the length of the total data file, in bytes.

Throws:

java.io.IOException - if an error occurs