CRAIIndexMerger (htsjdk 2.24.1 API)

java.lang.Object
- htsjdk.samtools.IndexMerger<CRAIIndex>
- - htsjdk.samtools.cram.CRAIIndexMerger

```
public final class CRAIIndexMerger
extends IndexMerger<CRAIIndex>
```
Merges CRAM index files for (headerless) parts of a CRAM file into a single index file. A partitioned CRAM is a directory containing the following files:
1. A file named header containing all header bytes (CRAM header and CRAM container containing the BAM header).
2. Zero or more files named part-00000, part-00001, ... etc, containing CRAM containers.
3. A file named terminator containing a CRAM end-of-file marker container.
If an index is required, a CRAM index can be generated for each (headerless) part file. These files should be named .part-00000.crai, .part-00001.crai, ... 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 CRAM file can be created from a partitioned CRAM file by merging all the non-hidden files (header, part-00000, part-00001, ..., terminator).
- A CRAM index can be created from a partitioned CRAM file by merging all of the hidden files with a .crai suffix. Note that this is not a simple file concatenation operation. See CRAIIndexMerger.

Field Summary
- Fields inherited from class htsjdk.samtools.IndexMerger
  out, partLengths

Constructor Summary

Constructors
Constructor Description

CRAIIndexMerger(OutputStream out, long headerLength)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finish(long dataFileLength)`	Finish merging the indexes, and close the output stream.
`void`	`processIndex(CRAIIndex 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
  - CRAIIndexMerger
```
public CRAIIndexMerger(OutputStream out,
                       long headerLength)
                throws IOException
```
    Throws:
    
    IOException
- Method Detail
  - processIndex
```
public void processIndex(CRAIIndex index,
                         long partLength)
```
    Description copied from class: IndexMerger
    
    Process the next index and add to the merged index.
    
    Specified by:
    
    processIndex in class IndexMerger<CRAIIndex>
    
    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 IOException
```
    Description copied from class: IndexMerger
    
    Finish merging the indexes, and close the output stream.
    
    Specified by:
    
    finish in class IndexMerger<CRAIIndex>
    
    Parameters:
    
    dataFileLength - the length of the total data file, in bytes.
    
    Throws:
    
    IOException - if an error occurs