Constant Field Values

Contents

• org.seqdoop.*

org.seqdoop.*

org.seqdoop.hadoop_bam.AnySAMInputFormat

Modifier and Type	Constant Field	Value
public static final String	TRUST_EXTS_PROPERTY	"hadoopbam.anysam.trust-exts"

org.seqdoop.hadoop_bam.AnySAMOutputFormat<K>

Modifier and Type	Constant Field	Value
public static final String	OUTPUT_SAM_FORMAT_PROPERTY	"hadoopbam.anysam.output-format"

org.seqdoop.hadoop_bam.BAMInputFormat

Modifier and Type	Constant Field	Value
public static final String	BOUNDED_TRAVERSAL_PROPERTY	"hadoopbam.bam.bounded-traversal"
public static final String	ENABLE_BAI_SPLIT_CALCULATOR	"hadoopbam.bam.enable-bai-splitter"
public static final String	INTERVALS_PROPERTY	"hadoopbam.bam.intervals"
public static final String	TRAVERSE_UNPLACED_UNMAPPED_PROPERTY	"hadoopbam.bam.traverse-unplaced-unmapped"

org.seqdoop.hadoop_bam.BAMOutputFormat<K>

Modifier and Type	Constant Field	Value
public static final String	WRITE_SPLITTING_BAI	"hadoopbam.bam.write-splitting-bai"

org.seqdoop.hadoop_bam.BAMSplitGuesser

Modifier and Type	Constant Field	Value
protected static final int	BGZF_MAGIC	67668767
protected static final int	BGZF_MAGIC_SUB	148290
protected static final int	BGZF_SUB_SIZE	6

org.seqdoop.hadoop_bam.BCFSplitGuesser

Modifier and Type	Constant Field	Value
protected static final int	BGZF_MAGIC	67668767
protected static final int	BGZF_MAGIC_SUB	148290
protected static final int	BGZF_SUB_SIZE	6

org.seqdoop.hadoop_bam.CRAMInputFormat

Modifier and Type	Constant Field	Value
public static final String	REFERENCE_SOURCE_PATH_PROPERTY	"hadoopbam.cram.reference-source-path"

org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader

Modifier and Type	Constant Field	Value
public static final int	MAX_LINE_LENGTH	20000

org.seqdoop.hadoop_bam.FastqInputFormat

Modifier and Type	Constant Field	Value
public static final String	CONF_BASE_QUALITY_ENCODING	"hbam.fastq-input.base-quality-encoding"
public static final String	CONF_BASE_QUALITY_ENCODING_DEFAULT	"sanger"
public static final String	CONF_FILTER_FAILED_QC	"hbam.fastq-input.filter-failed-qc"

org.seqdoop.hadoop_bam.FastqOutputFormat

Modifier and Type	Constant Field	Value
public static final String	CONF_BASE_QUALITY_ENCODING	"hbam.fastq-output.base-quality-encoding"
public static final String	CONF_BASE_QUALITY_ENCODING_DEFAULT	"sanger"

org.seqdoop.hadoop_bam.FormatConstants

Modifier and Type	Constant Field	Value
public static final String	CONF_INPUT_BASE_QUALITY_ENCODING	"hbam.input.base-quality-encoding"
public static final String	CONF_INPUT_FILTER_FAILED_QC	"hbam.input.filter-failed-qc"
public static final int	ILLUMINA_MAX	62
public static final int	ILLUMINA_OFFSET	64
public static final int	SANGER_MAX	93
public static final int	SANGER_OFFSET	33

org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat<K>

Modifier and Type	Constant Field	Value
public static final String	WRITE_HEADER_PROPERTY	"hadoopbam.anysam.write-header"

org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<K>

Modifier and Type	Constant Field	Value
public static final String	WRITE_HEADER_PROPERTY	"hadoopbam.vcf.write-header"

org.seqdoop.hadoop_bam.QseqInputFormat

Modifier and Type	Constant Field	Value
public static final String	CONF_BASE_QUALITY_ENCODING	"hbam.qseq-input.base-quality-encoding"
public static final String	CONF_BASE_QUALITY_ENCODING_DEFAULT	"illumina"
public static final String	CONF_FILTER_FAILED_QC	"hbam.qseq-input.filter-failed-qc"

org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader

Modifier and Type	Constant Field	Value
public static final int	MAX_LINE_LENGTH	20000

org.seqdoop.hadoop_bam.QseqOutputFormat

Modifier and Type	Constant Field	Value
public static final String	CONF_BASE_QUALITY_ENCODING	"hbam.qseq-output.base-quality-encoding"
public static final String	CONF_BASE_QUALITY_ENCODING_DEFAULT	"illumina"

org.seqdoop.hadoop_bam.SequencedFragment

Modifier and Type	Constant Field	Value
protected static final int	ControlNumber_Present	512
protected static final int	FilterPassed_Present	256
protected static final int	FlowcellId_Present	4
protected static final int	IndexSequence_Present	1024
protected static final int	Instrument_Present	1
protected static final int	Lane_Present	8
protected static final int	Read_Present	128
protected static final int	RunNumber_Present	2
protected static final int	Tile_Present	16
protected static final int	Xpos_Present	32
protected static final int	Ypos_Present	64

org.seqdoop.hadoop_bam.SplittingBAMIndexer

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_GRANULARITY	4096
public static final String	OUTPUT_FILE_EXTENSION	".splitting-bai"

org.seqdoop.hadoop_bam.VCFInputFormat

Modifier and Type	Constant Field	Value
public static final String	INTERVALS_PROPERTY	"hadoopbam.vcf.intervals"
public static final String	TRUST_EXTS_PROPERTY	"hadoopbam.vcf.trust-exts"

org.seqdoop.hadoop_bam.VCFOutputFormat<K>

Modifier and Type	Constant Field	Value
public static final String	OUTPUT_VCF_FORMAT_PROPERTY	"hadoopbam.vcf.output-format"

org.seqdoop.hadoop_bam.util.BGZFCodec

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_EXTENSION	".bgz"

org.seqdoop.hadoop_bam.util.SAMHeaderReader

Modifier and Type	Constant Field	Value
public static final String	VALIDATION_STRINGENCY_PROPERTY	"hadoopbam.samheaderreader.validation-stringency"