org.seqdoop.hadoop_bam

Class FormatConstants

java.lang.Object

org.seqdoop.hadoop_bam.FormatConstants

public class FormatConstants
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FormatConstants.BaseQualityEncoding Encodings for base quality formats.

Field Summary

Fields

Modifier and Type	Field and Description
static String	CONF_INPUT_BASE_QUALITY_ENCODING
static String	CONF_INPUT_FILTER_FAILED_QC
static int	ILLUMINA_MAX Maximum encodable quality score for Illumina Phred+64 encoded base qualities.
static int	ILLUMINA_OFFSET Offset by which Illumina-style ASCII-encoded quality scores are shifted.
static int	SANGER_MAX Maximum encodable quality score for Sanger Phred+33 encoded base qualities.
static int	SANGER_OFFSET Offset by which Sanger-style ASCII-encoded quality scores are shifted.

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

SANGER_OFFSET

public static final int SANGER_OFFSET

Offset by which Sanger-style ASCII-encoded quality scores are shifted.

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Constant Field Values

SANGER_MAX

public static final int SANGER_MAX

Maximum encodable quality score for Sanger Phred+33 encoded base qualities. Range of legal values is [0,93], according to wikipedia on 10/9/2013: http://en.wikipedia.org/wiki/FASTQ_format#Quality

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Constant Field Values

ILLUMINA_OFFSET

public static final int ILLUMINA_OFFSET

Offset by which Illumina-style ASCII-encoded quality scores are shifted.

See Also:

Constant Field Values

ILLUMINA_MAX

public static final int ILLUMINA_MAX

Maximum encodable quality score for Illumina Phred+64 encoded base qualities.

See Also:

Constant Field Values

CONF_INPUT_BASE_QUALITY_ENCODING

public static final String CONF_INPUT_BASE_QUALITY_ENCODING

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Constant Field Values

CONF_INPUT_FILTER_FAILED_QC

public static final String CONF_INPUT_FILTER_FAILED_QC

See Also:

Constant Field Values