htsjdk.samtools

Class BAMIndexMetaData

java.lang.Object

htsjdk.samtools.BAMIndexMetaData

public class BAMIndexMetaData
extends java.lang.Object

Metadata about the bam index contained within the bam index. One instance created per index file.

Method Summary

Methods

Modifier and Type	Method and Description
int	getAlignedRecordCount()
static BAMIndexMetaData[]	getIndexStats(htsjdk.samtools.BAMFileReader bam) Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
int	getUnalignedRecordCount()
static void	printIndexStats(java.io.File inputBamFile) Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getAlignedRecordCount

public int getAlignedRecordCount()

Returns:

the count of aligned records associated with this reference

getUnalignedRecordCount

public int getUnalignedRecordCount()

Returns:

the count of unaligned records associated with this reference

printIndexStats

public static void printIndexStats(java.io.File inputBamFile)

Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate

getIndexStats

public static BAMIndexMetaData[] getIndexStats(htsjdk.samtools.BAMFileReader bam)

Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate