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 Description

BAMIndexMerger(OutputStream out, long headerLength)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finish(long dataFileLength)`	Finish merging the indexes, and close the output stream.
`static BinningIndexContent.BinList`	`mergeBins(List<BinningIndexContent.BinList> binLists, long[] offsets)`	Merge bins for (headerless) BAM file parts.
`static LinearIndex`	`mergeLinearIndexes(int referenceSequence, 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(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(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,
                                             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

Class BAMIndexMerger

Field Summary

Fields inherited from class htsjdk.samtools.IndexMerger

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BAMIndexMerger

Method Detail

processIndex

finish

openIndex

mergeBins

mergeLinearIndexes