BAMIndexer (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.BAMIndexer

```
public class BAMIndexer
extends Object
```
Class for both constructing BAM index content and writing it out. There are two usage patterns: 1) Building a bam index from an existing bam file 2) Building a bam index while building the bam file In both cases, processAlignment is called for each alignment record and finish() is called at the end.

Constructor Summary

Constructors
Constructor and Description
`BAMIndexer(File output, SAMFileHeader fileHeader)`
`BAMIndexer(OutputStream output, SAMFileHeader fileHeader)` Prepare to index a BAM.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`createAndWriteIndex(File input, File output, boolean textOutput)` Generates a BAM index file, either textual or binary, from an input BAI file.
`static void`	`createIndex(SamReader reader, File output)` Generates a BAM index file from an input BAM file
`static void`	`createIndex(SamReader reader, File output, Log log)` Generates a BAM index file from an input BAM file
`void`	`finish()` After all the alignment records have been processed, finish is called.
`void`	`processAlignment(SAMRecord rec)` Record any index information for a given BAM record.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BAMIndexer
```
public BAMIndexer(File output,
                  SAMFileHeader fileHeader)
```
    Parameters:
    
    output - binary BAM Index (.bai) file
    
    fileHeader - header for the corresponding bam file
  - BAMIndexer
```
public BAMIndexer(OutputStream output,
                  SAMFileHeader fileHeader)
```
    Prepare to index a BAM.
    
    Parameters:
    
    output - Index will be written here. output will be closed when finish() method is called.
    
    fileHeader - header for the corresponding bam file.
- Method Detail
  - processAlignment
```
public void processAlignment(SAMRecord rec)
```
    Record any index information for a given BAM record. If this alignment starts a new reference, write out the old reference. Requires a non-null value for rec.getFileSource().
    
    Parameters:
    
    rec - The BAM record
  - finish
```
public void finish()
```
    After all the alignment records have been processed, finish is called. Writes any final information and closes the output file.
  - createAndWriteIndex
```
public static void createAndWriteIndex(File input,
                                       File output,
                                       boolean textOutput)
```
    Generates a BAM index file, either textual or binary, from an input BAI file. Only used for testing, but located here for visibility into CachingBAMFileIndex.
    
    Parameters:
    
    output - BAM Index (.bai) file (or bai.txt file when text)
    
    textOutput - Whether to create text output or binary
  - createIndex
```
public static void createIndex(SamReader reader,
                               File output)
```
    Generates a BAM index file from an input BAM file
    
    Parameters:
    
    reader - SamReader for input BAM file
    
    output - File for output index file
  - createIndex
```
public static void createIndex(SamReader reader,
                               File output,
                               Log log)
```
    Generates a BAM index file from an input BAM file
    
    Parameters:
    
    reader - SamReader for input BAM file
    
    output - File for output index file

Class BAMIndexer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BAMIndexer

BAMIndexer

Method Detail

processAlignment

finish

createAndWriteIndex

createIndex

createIndex