htsjdk.samtools

Class BAMIndexMerger

java.lang.Object

htsjdk.samtools.IndexMerger<AbstractBAMFileIndex>

htsjdk.samtools.BAMIndexMerger

public final class BAMIndexMerger
extends IndexMerger<AbstractBAMFileIndex>

Merges BAM index files for (headerless) parts of a BAM file into a single index file. The index files must have been produced using BAMIndexer with fillInUninitializedValues set to false. A partitioned BAM is a directory containing the following files:

1. A file named header containing all header bytes in BAM format.
2. Zero or more files named part-00000, part-00001, ... etc, containing a list of alignments in BAM format.
3. A file named terminator containing a BGZF end-of-file marker block.

If an index is required, a BAM index can be generated for each (headerless) part file. These files should be named .part-00000.bai, .part-00001.bai, ... 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 BAM file can be created from a partitioned BAM file by concatenating all the non-hidden files (header, part-00000, part-00001, ..., terminator).
• A BAM index can be created from a partitioned BAM file by merging all of the hidden files with a .bai suffix. Note that this is not a simple file concatenation operation. See BAMIndexMerger.

Field Summary

Fields inherited from class htsjdk.samtools.IndexMerger

out, partLengths

Constructor Summary

Constructors

Constructor and Description
BAMIndexMerger(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.
static BinningIndexContent.BinList	mergeBins(java.util.List<BinningIndexContent.BinList> binLists, long[] offsets) Merge bins for (headerless) BAM file parts.
static LinearIndex	mergeLinearIndexes(int referenceSequence, java.util.List<LinearIndex> linearIndexes, long[] offsets) Merge linear indexes for (headerless) BAM file parts.
static AbstractBAMFileIndex	openIndex(SeekableStream stream, SAMSequenceDictionary dictionary)
void	processIndex(AbstractBAMFileIndex 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

BAMIndexMerger

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

Method Detail

processIndex

public void processIndex(AbstractBAMFileIndex index,
                         long partLength)

Description copied from class: IndexMerger

Process the next index and add to the merged index.

Specified by:

processIndex in class IndexMerger<AbstractBAMFileIndex>

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)

Description copied from class: IndexMerger

Finish merging the indexes, and close the output stream.

Specified by:

finish in class IndexMerger<AbstractBAMFileIndex>

Parameters:

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

openIndex

public static AbstractBAMFileIndex openIndex(SeekableStream stream,
                                             SAMSequenceDictionary dictionary)

mergeBins

public static BinningIndexContent.BinList mergeBins(java.util.List<BinningIndexContent.BinList> binLists,
                                                    long[] offsets)

Merge bins for (headerless) BAM file parts.

Parameters:

binLists - the bins to merge

offsets - bin i will be shifted by offset i

Returns:

the merged bins

mergeLinearIndexes

public static LinearIndex mergeLinearIndexes(int referenceSequence,
                                             java.util.List<LinearIndex> linearIndexes,
                                             long[] offsets)

Merge linear indexes for (headerless) BAM file parts.

Parameters:

referenceSequence - the reference sequence number for the linear indexes being merged

linearIndexes - the linear indexes to merge

offsets - linear index i will be shifted by offset i

Returns:

the merged linear index