htsjdk.samtools

Class BAMIndexer

java.lang.Object

htsjdk.samtools.BAMIndexer

public class BAMIndexer
extends java.lang.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(java.io.File output, SAMFileHeader fileHeader)
BAMIndexer(java.io.OutputStream output, SAMFileHeader fileHeader) Prepare to index a BAM.

Method Summary

Methods

Modifier and Type	Method and Description
static void	createAndWriteIndex(java.io.File input, java.io.File output, boolean textOutput) Generates a BAM index file, either textual or binary, from an input BAI file.
static void	createIndex(SamReader reader, java.io.File output) Generates a BAM index file from an input BAM file
static void	createIndex(SamReader reader, java.io.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(java.io.File output,
          SAMFileHeader fileHeader)

Parameters:

output - binary BAM Index (.bai) file

fileHeader - header for the corresponding bam file

BAMIndexer

public BAMIndexer(java.io.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(java.io.File input,
                       java.io.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,
               java.io.File output)

Generates a BAM index file from an input BAM file

Parameters:

reader - SAMFileReader for input BAM file

output - File for output index file

createIndex

public static void createIndex(SamReader reader,
               java.io.File output,
               Log log)

Generates a BAM index file from an input BAM file

Parameters:

reader - SAMFileReader for input BAM file

output - File for output index file