Package htsjdk.samtools
Class BAMIndexMetaData
- java.lang.Object
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- htsjdk.samtools.BAMIndexMetaData
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public class BAMIndexMetaData extends Object
Metadata about the bam index contained within the bam index. One instance created per index file.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getAlignedRecordCount()
static BAMIndexMetaData[]
getIndexStats(BAMFileReader bam)
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinateint
getUnalignedRecordCount()
static void
printIndexStats(File inputBamFile)
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
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Method Detail
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getAlignedRecordCount
public int getAlignedRecordCount()
- Returns:
- the count of aligned records associated with this reference
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getUnalignedRecordCount
public int getUnalignedRecordCount()
- Returns:
- the count of unaligned records associated with this reference
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printIndexStats
public static void printIndexStats(File inputBamFile)
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
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getIndexStats
public static BAMIndexMetaData[] getIndexStats(BAMFileReader bam)
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
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