Constant Field Values

Contents

• htsjdk.beta.*
• htsjdk.samtools.*
• htsjdk.tribble.*
• htsjdk.variant.*

htsjdk.beta.*

htsjdk.beta.codecs.reads.bam.BAMEncoderOptions

Modifier and Type	Constant Field	Value
public static final int	DEAFULT_MAX_RECORDS_IN_RAM	500000

htsjdk.beta.io.bundle.BundleJSON

Modifier and Type	Constant Field	Value
public static final String	BUNDLE_EXTENSION	".json"
public static final String	JSON_PROPERTY_FORMAT	"format"
public static final String	JSON_PROPERTY_PATH	"path"
public static final String	JSON_PROPERTY_PRIMARY	"primary"
public static final String	JSON_PROPERTY_SCHEMA	"schema"
public static final String	JSON_PROPERTY_SCHEMA_NAME	"schemaName"
public static final String	JSON_PROPERTY_SCHEMA_VERSION	"schemaVersion"
public static final String	JSON_SCHEMA_NAME	"htsbundle"
public static final String	JSON_SCHEMA_VERSION	"0.1.0"

htsjdk.beta.io.bundle.BundleResourceType

Modifier and Type	Constant Field	Value
public static final String	CT_ALIGNED_READS	"ALIGNED_READS"
public static final String	CT_FEATURES	"FEATURES"
public static final String	CT_HAPLOID_REFERENCE	"HAPLOID_REFERENCE"
public static final String	CT_MD5	"MD5"
public static final String	CT_READS_INDEX	"READS_INDEX"
public static final String	CT_REFERENCE_DICTIONARY	"REFERENCE_DICTIONARY"
public static final String	CT_REFERENCE_INDEX	"REFERENCE_INDEX"
public static final String	CT_VARIANT_CONTEXTS	"VARIANT_CONTEXTS"
public static final String	CT_VARIANTS_INDEX	"VARIANTS_INDEX"
public static final String	FMT_READS_BAM	"BAM"
public static final String	FMT_READS_CRAM	"CRAM"
public static final String	FMT_READS_HTSGET_BAM	"HTSGET_BAM"
public static final String	FMT_READS_INDEX_BAI	"BAI"
public static final String	FMT_READS_INDEX_CRAI	"CRAI"
public static final String	FMT_READS_INDEX_CSI	"CSI"
public static final String	FMT_READS_SAM	"SAM"
public static final String	FMT_VARIANTS_BCF	"BCF"
public static final String	FMT_VARIANTS_VCF	"VCF"

htsjdk.beta.plugin.hapref.HaploidReferenceFormats

Modifier and Type	Constant Field	Value
public static final String	FASTA	"FASTA"

htsjdk.beta.plugin.reads.ReadsFormats

Modifier and Type	Constant Field	Value
public static final String	BAM	"BAM"
public static final String	CRAM	"CRAM"
public static final String	HTSGET_BAM	"HTSGET_BAM"
public static final String	SAM	"SAM"

htsjdk.beta.plugin.variants.VariantsFormats

Modifier and Type	Constant Field	Value
public static final String	BCF	"BCF"
public static final String	VCF	"VCF"

htsjdk.samtools.*

htsjdk.samtools.AbstractSAMHeaderRecord

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.AlignmentBlock

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.BamFileIoUtils

Modifier and Type	Constant Field	Value
public static final String	BAM_FILE_EXTENSION	".bam"

htsjdk.samtools.BAMIndex

Modifier and Type	Constant Field	Value
public static final String	BAI_INDEX_SUFFIX	".bai"
public static final String	BAMIndexSuffix	".bai"
public static final String	CSI_INDEX_SUFFIX	".csi"

htsjdk.samtools.BAMRecord

Modifier and Type	Constant Field	Value
public static final short	CIGAR_SIZE_MULTIPLIER	4
public static final int	MAX_CIGAR_ELEMENT_LENGTH	268435455
public static final int	MAX_CIGAR_OPERATORS	65535

htsjdk.samtools.Cigar

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.CigarElement

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.Defaults

Modifier and Type	Constant Field	Value
public static final String	DISABLE_SNAPPY_PROPERTY_NAME	"snappy.disable"
public static final String	OPTIMISTIC_VCF_4_4_PROPERTY	"optimistic_vcf_4_4"
public static final String	SAMJDK_PREFIX	"samjdk."

htsjdk.samtools.DownsamplingIteratorFactory

Modifier and Type	Constant Field	Value
public static final String	CHAINED_DESCRIPTION	"Attempts to provide a compromise strategy that offers some of the advantages of both the ConstantMemory and HighAccuracy strategies. Uses a ConstantMemory strategy to downsample the incoming stream to approximately the desired proportion, and then a HighAccuracy strategy to finish. Works in a single pass, and will provide accuracy close to (but often not as good as) HighAccuracy while requiring memory proportional to the set of reads emitted from the ConstantMemory strategy to the HighAccuracy strategy. Works well when downsampling large inputs to small proportions (e.g. downsampling hundreds of millions of reads and retaining only 2%. Should be accurate 99.9% of the time when the input contains more than 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead."
public static final String	CONSTANT_MEMORY_DESCRPTION	"Downsamples a stream or file of SAMRecords using a hash-projection strategy such that it can run in constant memory. The downsampling is stochastic, and therefore the actual retained proportion will vary around the requested proportion. Due to working in fixed memory this strategy is good for large inputs, and due to the stochastic nature the accuracy of this strategy is highest with a high number of output records, and diminishes at low output volumes."
public static final String	HIGH_ACCURACY_DESCRIPTION	"Attempts (but does not guarantee) to provide accuracy up to a specified limit. Accuracy is defined as emitting a proportion of reads as close to the requested proportion as possible. In order to do so this strategy requires memory that is proportional to the number of template names in the incoming stream of reads, and will thus require large amounts of memory when running on large input files."

htsjdk.samtools.GenomicIndexUtil

Modifier and Type	Constant Field	Value
public static final int	BIN_GENOMIC_SPAN	536870912
public static final int	MAX_BINS	37450
public static final int	UNSET_GENOMIC_LOCATION	0

htsjdk.samtools.HtsgetBAMFileReader

Modifier and Type	Constant Field	Value
public static final String	HTSGET_SCHEME	"htsget"

htsjdk.samtools.LinearIndex

Modifier and Type	Constant Field	Value
public static final int	BAM_LIDX_SHIFT	14

htsjdk.samtools.ReservedTagConstants

Modifier and Type	Constant Field	Value
public static final String	OC	"OC"
public static final String	XF	"XF"
public static final String	XN	"XN"
public static final String	XQ	"XQ"
public static final String	XS	"XS"
public static final String	XT	"XT"

htsjdk.samtools.SAMBinaryTagAndValue

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.SAMFileHeader

Modifier and Type	Constant Field	Value
public static final String	CURRENT_VERSION	"1.6"
public static final String	GROUP_ORDER_TAG	"GO"
public static final String	SORT_ORDER_TAG	"SO"
public static final String	VERSION_TAG	"VN"

htsjdk.samtools.SamFileValidator

Modifier and Type	Constant Field	Value
public static final int	MAX_QUALITY_NOT_STORED_ERRORS	100

htsjdk.samtools.SAMProgramRecord

Modifier and Type	Constant Field	Value
public static final String	COMMAND_LINE_TAG	"CL"
public static final String	PREVIOUS_PROGRAM_GROUP_ID_TAG	"PP"
public static final String	PROGRAM_GROUP_ID_TAG	"ID"
public static final String	PROGRAM_NAME_TAG	"PN"
public static final String	PROGRAM_VERSION_TAG	"VN"

htsjdk.samtools.SAMReadGroupRecord

Modifier and Type	Constant Field	Value
public static final String	BARCODE_TAG	"BC"
public static final String	DATE_RUN_PRODUCED_TAG	"DT"
public static final String	DESCRIPTION_TAG	"DS"
public static final String	FLOW_ORDER_TAG	"FO"
public static final String	KEY_SEQUENCE_TAG	"KS"
public static final String	LIBRARY_TAG	"LB"
public static final String	PLATFORM_MODEL_TAG	"PM"
public static final String	PLATFORM_TAG	"PL"
public static final String	PLATFORM_UNIT_TAG	"PU"
public static final String	PREDICTED_MEDIAN_INSERT_SIZE_TAG	"PI"
public static final String	PROGRAM_GROUP_TAG	"PG"
public static final String	READ_GROUP_ID_TAG	"ID"
public static final String	READ_GROUP_SAMPLE_TAG	"SM"
public static final String	SEQUENCING_CENTER_TAG	"CN"

htsjdk.samtools.SAMRecord

Modifier and Type	Constant Field	Value
public static final int	MAX_INSERT_SIZE	2147483647
public static final String	NO_ALIGNMENT_CIGAR	"*"
public static final int	NO_ALIGNMENT_REFERENCE_INDEX	-1
public static final String	NO_ALIGNMENT_REFERENCE_NAME	"*"
public static final int	NO_ALIGNMENT_START	0
public static final int	NO_MAPPING_QUALITY	0
public static final String	NULL_QUALS_STRING	"*"
public static final String	NULL_SEQUENCE_STRING	"*"
public static final long	serialVersionUID	1L
public static final int	UNKNOWN_MAPPING_QUALITY	255

htsjdk.samtools.SAMRecordDuplicateComparator

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_LIBRARY_STRING	"Unknown Library"

htsjdk.samtools.SAMRecordSetBuilder

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CHROMOSOME_LENGTH	200000000

htsjdk.samtools.SAMSequenceDictionary

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.SAMSequenceRecord

Modifier and Type	Constant Field	Value
public static final String	ALTERNATIVE_SEQUENCE_NAME_TAG	"AN"
public static final String	ASSEMBLY_TAG	"AS"
public static final String	DESCRIPTION_TAG	"DS"
public static final String	MD5_TAG	"M5"
public static final String	RESERVED_MRNM_SEQUENCE_NAME	"="
public static final String	RESERVED_RNEXT_SEQUENCE_NAME	"="
public static final String	SEQUENCE_LENGTH_TAG	"LN"
public static final String	SEQUENCE_NAME_TAG	"SN"
public static final long	serialVersionUID	1L
public static final String	SPECIES_TAG	"SP"
public static final int	UNAVAILABLE_SEQUENCE_INDEX	-1
public static final int	UNKNOWN_SEQUENCE_LENGTH	0
public static final String	URI_TAG	"UR"

htsjdk.samtools.SAMUtils

Modifier and Type	Constant Field	Value
public static final int	MAX_PHRED_SCORE	93

htsjdk.samtools.SAMValidationError

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.samtools.SBIIndex

Modifier and Type	Constant Field	Value
public static final String	FILE_EXTENSION	".sbi"

htsjdk.samtools.SBIIndexWriter

Modifier and Type	Constant Field	Value
public static final long	DEFAULT_GRANULARITY	4096L

htsjdk.samtools.SQTagUtil

Modifier and Type	Constant Field	Value
public static final byte	MAX_QUALITY	0x3f

htsjdk.samtools.SRAIndex

Modifier and Type	Constant Field	Value
public static final int	SRA_BIN_SIZE	16384
public static final int	SRA_CHUNK_SIZE	50000

htsjdk.samtools.cram.CRAIIndex

Modifier and Type	Constant Field	Value
public static final String	CRAI_INDEX_SUFFIX	".crai"

htsjdk.samtools.cram.build.CompressionHeaderFactory

Modifier and Type	Constant Field	Value
public static final int	ALL_BYTES_USED	-1
public static final int	BYTE_SPACE_SIZE	256

htsjdk.samtools.cram.build.CramIO

Modifier and Type	Constant Field	Value
public static final String	CRAM_FILE_EXTENSION	".cram"
public static final int	EOF_ALIGNMENT_SPAN	0
public static final int	EOF_ALIGNMENT_START	4542278
public static final int	EOF_BLOCK_SIZE_V2	11
public static final int	EOF_BLOCK_SIZE_V3	15

htsjdk.samtools.cram.build.CRAMReferenceRegion

Modifier and Type	Constant Field	Value
public static final int	UNINITIALIZED_LENGTH	-1
public static final int	UNINITIALIZED_START	-1

htsjdk.samtools.cram.compression.ExternalCompressor

Modifier and Type	Constant Field	Value
public static final int	NO_COMPRESSION_ARG	-1

htsjdk.samtools.cram.compression.rans.RANS

Modifier and Type	Constant Field	Value
public static final int	NUMBER_OF_SYMBOLS	256

htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore

Modifier and Type	Constant Field	Value
public static final byte	operator	0x51

htsjdk.samtools.cram.encoding.readfeatures.Bases

Modifier and Type	Constant Field	Value
public static final byte	operator	0x62

htsjdk.samtools.cram.encoding.readfeatures.Deletion

Modifier and Type	Constant Field	Value
public static final byte	operator	0x44

htsjdk.samtools.cram.encoding.readfeatures.HardClip

Modifier and Type	Constant Field	Value
public static final byte	operator	0x48

htsjdk.samtools.cram.encoding.readfeatures.InsertBase

Modifier and Type	Constant Field	Value
public static final byte	operator	0x69

htsjdk.samtools.cram.encoding.readfeatures.Insertion

Modifier and Type	Constant Field	Value
public static final byte	operator	0x49

htsjdk.samtools.cram.encoding.readfeatures.Padding

Modifier and Type	Constant Field	Value
public static final byte	operator	0x50

htsjdk.samtools.cram.encoding.readfeatures.ReadBase

Modifier and Type	Constant Field	Value
public static final byte	operator	0x42

htsjdk.samtools.cram.encoding.readfeatures.RefSkip

Modifier and Type	Constant Field	Value
public static final byte	operator	0x4e

htsjdk.samtools.cram.encoding.readfeatures.Scores

Modifier and Type	Constant Field	Value
public static final byte	operator	0x71

htsjdk.samtools.cram.encoding.readfeatures.SoftClip

Modifier and Type	Constant Field	Value
public static final byte	operator	0x53

htsjdk.samtools.cram.encoding.readfeatures.Substitution

Modifier and Type	Constant Field	Value
public static final int	NO_CODE	-1
public static final byte	operator	0x58

htsjdk.samtools.cram.io.ITF8

Modifier and Type	Constant Field	Value
public static final int	MAX_BYTES	5

htsjdk.samtools.cram.ref.ReferenceContext

Modifier and Type	Constant Field	Value
public static final int	MULTIPLE_REFERENCE_ID	-2
public static final int	UNINITIALIZED_REFERENCE_ID	-3
public static final int	UNMAPPED_UNPLACED_ID	-1

htsjdk.samtools.cram.structure.AlignmentContext

Modifier and Type	Constant Field	Value
public static final int	NO_ALIGNMENT_END	0
public static final int	NO_ALIGNMENT_SPAN	0
public static final int	NO_ALIGNMENT_START	0

htsjdk.samtools.cram.structure.CRAMCompressionRecord

Modifier and Type	Constant Field	Value
public static final int	CF_DETACHED	2
public static final int	CF_HAS_MATE_DOWNSTREAM	4
public static final int	CF_QS_PRESERVED_AS_ARRAY	1
public static final int	CF_UNKNOWN_BASES	8
public static final int	MF_MATE_NEG_STRAND	1
public static final int	MF_MATE_UNMAPPED	2
public static final byte	MISSING_QUALITY_SCORE	0xff
public static final int	NO_READGROUP_ID	-1

htsjdk.samtools.cram.structure.CRAMEncodingStrategy

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD	1000
public static final int	DEFAULT_READS_PER_SLICE	10000

htsjdk.samtools.cram.structure.CramHeader

Modifier and Type	Constant Field	Value
public static final int	CRAM_ID_LENGTH	20
public static final int	CRAM_VERSION_LENGTH	2

htsjdk.samtools.cram.structure.Slice

Modifier and Type	Constant Field	Value
public static final int	EMBEDDED_REFERENCE_ABSENT_CONTENT_ID	-1
public static final int	UNINITIALIZED_INDEXING_PARAMETER	-1

htsjdk.samtools.cram.structure.block.Block

Modifier and Type	Constant Field	Value
public static final int	NO_CONTENT_ID	0

htsjdk.samtools.fastq.FastqConstants

Modifier and Type	Constant Field	Value
public static final String	FIRST_OF_PAIR	"/1"
public static final String	QUALITY_HEADER	"+"
public static final String	SECOND_OF_PAIR	"/2"
public static final String	SEQUENCE_HEADER	"@"

htsjdk.samtools.filter.AbstractJavascriptFilter<HEADER,TYPE>

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_HEADER_KEY	"header"

htsjdk.samtools.liftover.LiftOver

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_LIFTOVER_MINMATCH	0.95

htsjdk.samtools.metrics.MetricsFile<BEAN extends MetricBase,HKEY extends Comparable>

Modifier and Type	Constant Field	Value
public static final String	HISTO_HEADER	"## HISTOGRAM\t"
public static final String	MAJOR_HEADER_PREFIX	"## "
public static final String	METRIC_HEADER	"## METRICS CLASS\t"
public static final String	MINOR_HEADER_PREFIX	"# "
public static final String	SEPARATOR	"\t"

htsjdk.samtools.reference.FastaReferenceWriter

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BASES_PER_LINE	60
public static final char	HEADER_NAME_AND_DESCRIPTION_SEPARATOR	' '
public static final char	HEADER_START_CHAR	'>'

htsjdk.samtools.reference.ReferenceSequenceFileFactory

Modifier and Type	Constant Field	Value
public static final String	FASTA_INDEX_EXTENSION	".fai"

htsjdk.samtools.seekablestream.SeekableBufferedStream

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BUFFER_SIZE	512000

htsjdk.samtools.seekablestream.SeekableStreamFactory

Modifier and Type	Constant Field	Value
public static final String	FILE_SCHEME	"file"

htsjdk.samtools.sra.SRAUtils

Modifier and Type	Constant Field	Value
public static final int	REFERENCE_ALIGNMENT	5000

htsjdk.samtools.util.AbstractAsyncWriter<T>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_QUEUE_SIZE	2000

htsjdk.samtools.util.BinaryCodec

Modifier and Type	Constant Field	Value
public static final long	MAX_UBYTE	255L
public static final long	MAX_UINT	4294967295L
public static final long	MAX_USHORT	65535L

htsjdk.samtools.util.BlockCompressedFilePointerUtil

Modifier and Type	Constant Field	Value
public static final long	MAX_BLOCK_ADDRESS	281474976710655L
public static final int	MAX_OFFSET	65535

htsjdk.samtools.util.BlockCompressedInputStream

Modifier and Type	Constant Field	Value
public static final String	CANNOT_SEEK_CLOSED_STREAM_MSG	"Cannot seek a position for a closed stream"
public static final String	CANNOT_SEEK_STREAM_MSG	"Cannot seek a position for a non-file stream"
public static final String	INCORRECT_HEADER_SIZE_MSG	"Incorrect header size for file: "
public static final String	INVALID_FILE_PTR_MSG	"Invalid file pointer: "
public static final String	PREMATURE_END_MSG	"Premature end of file: "
public static final String	UNEXPECTED_BLOCK_LENGTH_MSG	"Unexpected compressed block length: "

htsjdk.samtools.util.BlockCompressedStreamConstants

Modifier and Type	Constant Field	Value
public static final byte	BGZF_ID1	0x42
public static final byte	BGZF_ID2	0x43
public static final byte	BGZF_LEN	0x2
public static final int	BLOCK_FOOTER_LENGTH	8
public static final int	BLOCK_HEADER_LENGTH	18
public static final int	BLOCK_LENGTH_OFFSET	16
public static final int	DEFAULT_UNCOMPRESSED_BLOCK_SIZE	65498
public static final byte	GZIP_CM_DEFLATE	0x8
public static final int	GZIP_FLG	4
public static final byte	GZIP_ID1	0x1f
public static final int	GZIP_ID2	139
public static final int	GZIP_OS_UNKNOWN	255
public static final int	GZIP_OVERHEAD	28
public static final int	GZIP_XFL	0
public static final short	GZIP_XLEN	6
public static final int	MAX_COMPRESSED_BLOCK_SIZE	65536
public static final int	NO_COMPRESSION_OVERHEAD	10

htsjdk.samtools.util.FileExtensions

Modifier and Type	Constant Field	Value
public static final String	BAI_INDEX	".bai"
public static final String	BAM	".bam"
public static final String	BCF	".bcf"
public static final String	BED	".bed"
public static final String	COMPRESSED_INTERVAL_LIST	".interval_list.gz"
public static final String	COMPRESSED_VCF	".vcf.gz"
public static final String	COMPRESSED_VCF_INDEX	".tbi"
public static final String	CRAM	".cram"
public static final String	CRAM_INDEX	".crai"
public static final String	CSI	".csi"
public static final String	DICT	".dict"
public static final String	FASTA_INDEX	".fai"
public static final String	GZI	".gzi"
public static final String	INTERVAL_LIST	".interval_list"
public static final String	MD5	".md5"
public static final String	SAM	".sam"
public static final String	SBI	".sbi"
public static final String	TABIX_INDEX	".tbi"
public static final String	TRIBBLE_INDEX	".idx"
public static final String	VCF	".vcf"
public static final String	VCF_INDEX	".idx"

htsjdk.samtools.util.FormatUtil

Modifier and Type	Constant Field	Value
public static final int	DECIMAL_DIGITS_TO_PRINT	6

htsjdk.samtools.util.GZIIndex

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

htsjdk.samtools.util.IntervalList

Modifier and Type	Constant Field	Value
public static final String	INTERVAL_LIST_FILE_EXTENSION	".interval_list"

htsjdk.samtools.util.IntervalTree.Node<V1>

Modifier and Type	Constant Field	Value
public static final int	HAS_GREATER_PART	4
public static final int	HAS_LESSER_PART	1
public static final int	HAS_OVERLAPPING_PART	2
public static final int	IS_ADJACENT_AND_EMPTY	0
public static final int	IS_LEFT_OVERHANGING_OVERLAPPER	3
public static final int	IS_RIGHT_OVERHANGING_OVERLAPPER	6
public static final int	IS_STRICTLY_GREATER	4
public static final int	IS_STRICTLY_LESS	1
public static final int	IS_SUBSET	2
public static final int	IS_SUPERSET	7

htsjdk.samtools.util.IOUtil

Modifier and Type	Constant Field	Value
public static final String	BCF_FILE_EXTENSION	".bcf"
public static final String	COMPRESSED_VCF_FILE_EXTENSION	".vcf.gz"
public static final String	COMPRESSED_VCF_INDEX_EXTENSION	".tbi"
public static final String	DICT_FILE_EXTENSION	".dict"
public static final long	FIVE_GBS	5368709120L
public static final int	GZIP_HEADER_READ_LENGTH	8000
public static final String	INTERVAL_LIST_FILE_EXTENSION	".interval_list"
public static final long	ONE_GB	1073741824L
public static final String	SAM_FILE_EXTENSION	".sam"
public static final long	TWO_GBS	2147483648L
public static final String	VCF_FILE_EXTENSION	".vcf"
public static final String	VCF_INDEX_EXTENSION	".idx"

htsjdk.samtools.util.LineReader

Modifier and Type	Constant Field	Value
public static final int	EOF_VALUE	-1

htsjdk.samtools.util.QualityEncodingDetector

Modifier and Type	Constant Field	Value
public static final long	DEFAULT_MAX_RECORDS_TO_ITERATE	10000L

htsjdk.samtools.util.RelativeIso8601Date

Modifier and Type	Constant Field	Value
public static final String	LAZY_NOW_LABEL	"NOW"

htsjdk.samtools.util.SamConstants

Modifier and Type	Constant Field	Value
public static final String	BARCODE_QUALITY_DELIMITER	" "
public static final String	BARCODE_SEQUENCE_DELIMITER	"-"

htsjdk.samtools.util.SequenceUtil

Modifier and Type	Constant Field	Value
public static final byte	a	0x61
public static final byte	A	0x41
public static final byte	c	0x63
public static final byte	C	0x43
public static final byte	g	0x67
public static final byte	G	0x47
public static final byte	n	0x6e
public static final byte	N	0x4e
public static final byte	t	0x74
public static final byte	T	0x54

htsjdk.samtools.util.SolexaQualityConverter

Modifier and Type	Constant Field	Value
public static final int	ILLUMINA_TO_PHRED_SUBTRAHEND	31
public static final int	PHRED_ADDEND	33
public static final int	SOLEXA_ADDEND	64

htsjdk.samtools.util.SortingLongCollection

Modifier and Type	Constant Field	Value
public static final int	SIZEOF	8

htsjdk.samtools.util.StringUtil

Modifier and Type	Constant Field	Value
public static final String	EMPTY_STRING	""

htsjdk.samtools.util.TestUtil

Modifier and Type	Constant Field	Value
public static final String	BASE_URL_FOR_HTTP_TESTS	"https://personal.broadinstitute.org/picard/testdata/"
public static final int	RANDOM_SEED	42

htsjdk.samtools.util.ftp.FTPClient

Modifier and Type	Constant Field	Value
public static final int	READ_TIMEOUT	300000

htsjdk.samtools.util.htsget.HtsgetRequest

Modifier and Type	Constant Field	Value
protected static final String	ACCEPT_TYPE	"application/vnd.ga4gh.htsget.v1.2.0+json"
protected static final String	PROTOCOL_VERSION	"vnd.ga4gh.htsget.v1.2.0"

htsjdk.tribble.*

htsjdk.tribble.FeatureCodecHeader

Modifier and Type	Constant Field	Value
public static final long	NO_HEADER_END	0L

htsjdk.tribble.Tribble

Modifier and Type	Constant Field	Value
public static final String	STANDARD_INDEX_EXTENSION	".idx"

htsjdk.tribble.bed.BEDCodec

Modifier and Type	Constant Field	Value
public static final String	BED_EXTENSION	".bed"

htsjdk.tribble.example.ExampleBinaryCodec

Modifier and Type	Constant Field	Value
public static final String	HEADER_LINE	"# BinaryTestFeature"

htsjdk.tribble.gff.Gff3Constants

Modifier and Type	Constant Field	Value
public static final String	ALIAS_ATTRIBUTE_KEY	"Alias"
public static final char	ATTRIBUTE_DELIMITER	';'
public static final String	COMMENT_START	"#"
public static final String	DIRECTIVE_START	"##"
public static final char	END_OF_LINE_CHARACTER	'\n'
public static final char	FIELD_DELIMITER	'\t'
public static final String	ID_ATTRIBUTE_KEY	"ID"
public static final char	KEY_VALUE_SEPARATOR	'='
public static final String	NAME_ATTRIBUTE_KEY	"Name"
public static final String	PARENT_ATTRIBUTE_KEY	"Parent"
public static final String	UNDEFINED_FIELD_VALUE	"."
public static final char	VALUE_DELIMITER	','

htsjdk.tribble.index.AbstractIndex

Modifier and Type	Constant Field	Value
public static final int	MAGIC_NUMBER	1480870228
public static final int	VERSION	3

htsjdk.tribble.index.interval.IntervalIndexCreator

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_FEATURE_COUNT	600

htsjdk.tribble.index.linear.LinearIndexCreator

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BIN_WIDTH	8000

htsjdk.tribble.index.tabix.TabixFormat

Modifier and Type	Constant Field	Value
public static final int	GENERIC_FLAGS	0
public static final int	SAM_FLAGS	1
public static final int	UCSC_FLAGS	65536
public static final int	VCF_FLAGS	2
public static final int	ZERO_BASED	65536

htsjdk.tribble.util.TabixUtils

Modifier and Type	Constant Field	Value
public static final String	STANDARD_INDEX_EXTENSION	".tbi"

htsjdk.variant.*

htsjdk.variant.bcf2.BCF2Codec

Modifier and Type	Constant Field	Value
protected static final int	ALLOWED_MAJOR_VERSION	2
protected static final int	ALLOWED_MINOR_VERSION	1

htsjdk.variant.bcf2.BCF2Utils

Modifier and Type	Constant Field	Value
public static final int	MAX_ALLELES_IN_GENOTYPES	127
public static final int	MAX_INLINE_ELEMENTS	14
public static final int	OVERFLOW_ELEMENT_MARKER	15

htsjdk.variant.utils.GeneralUtils

Modifier and Type	Constant Field	Value
public static final boolean	DEBUG_MODE_ENABLED	false
public static final double	LOG10_P_OF_ZERO	-1000000.0

htsjdk.variant.variantcontext.Allele

Modifier and Type	Constant Field	Value
public static final char	BREAKEND_EXTENDING_LEFT	']'
public static final char	BREAKEND_EXTENDING_RIGHT	'['
public static final String	NO_CALL_STRING	"."
public static final String	NON_REF_STRING	"<NON_REF>"
public static final char	SINGLE_BREAKEND_INDICATOR	'.'
public static final String	SPAN_DEL_STRING	"*"
public static final char	SYMBOLIC_ALLELE_END	'>'
public static final char	SYMBOLIC_ALLELE_START	'<'
public static final String	UNSPECIFIED_ALTERNATE_ALLELE_STRING	"<*>"

htsjdk.variant.variantcontext.CommonInfo

Modifier and Type	Constant Field	Value
public static final double	NO_LOG10_PERROR	1.0
public static final long	serialVersionUID	1L

htsjdk.variant.variantcontext.Genotype

Modifier and Type	Constant Field	Value
public static final String	PHASED_ALLELE_SEPARATOR	"|"
public static final long	serialVersionUID	1L
public static final String	UNPHASED_ALLELE_SEPARATOR	"/"

htsjdk.variant.variantcontext.GenotypeLikelihoods

Modifier and Type	Constant Field	Value
public static final int	MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED	50
public static final int	MAX_PL	2147483647

htsjdk.variant.variantcontext.GenotypesContext

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

htsjdk.variant.variantcontext.VariantContext

Modifier and Type	Constant Field	Value
public static final double	NO_LOG10_PERROR	1.0
public static final long	serialVersionUID	1L

htsjdk.variant.variantcontext.writer.BCF2Encoder

Modifier and Type	Constant Field	Value
public static final int	WRITE_BUFFER_INITIAL_SIZE	16384

htsjdk.variant.variantcontext.writer.SortingVariantContextWriter

Modifier and Type	Constant Field	Value
protected static final int	BEFORE_MOST_UPSTREAM_LOC	0

htsjdk.variant.vcf.AbstractVCFCodec

Modifier and Type	Constant Field	Value
protected static final int	NUM_STANDARD_FIELDS	8

htsjdk.variant.vcf.VCF3Codec

Modifier and Type	Constant Field	Value
public static final String	VCF3_MAGIC_HEADER	"##fileformat=VCFv3"

htsjdk.variant.vcf.VCFCodec

Modifier and Type	Constant Field	Value
public static final String	VCF4_MAGIC_HEADER	"##fileformat=VCFv4"

htsjdk.variant.vcf.VCFConstants

Modifier and Type	Constant Field	Value
public static final String	ALLELE_COUNT_KEY	"AC"
public static final String	ALLELE_FREQUENCY_KEY	"AF"
public static final String	ALLELE_NUMBER_KEY	"AN"
public static final String	ALT_HEADER_KEY	"ALT"
public static final String	ALT_HEADER_START	"##ALT"
public static final String	ANCESTRAL_ALLELE_KEY	"AA"
public static final String	CIGAR_KEY	"CIGAR"
public static final String	CONTIG_HEADER_KEY	"contig"
public static final String	CONTIG_HEADER_START	"##contig"
public static final String	DBSNP_KEY	"DB"
public static final char	DELETION_ALLELE_v3	'D'
public static final String	DEPTH_KEY	"DP"
public static final String	EMPTY_ALLELE	"."
public static final String	EMPTY_ALTERNATE_ALLELE_FIELD	"."
public static final String	EMPTY_GENOTYPE	"./."
public static final String	EMPTY_ID_FIELD	"."
public static final String	EMPTY_INFO_FIELD	"."
public static final String	END_KEY	"END"
public static final String	EXPECTED_ALLELE_COUNT_KEY	"EC"
public static final String	FIELD_SEPARATOR	"\t"
public static final char	FIELD_SEPARATOR_CHAR	'\t'
public static final String	FILTER_CODE_SEPARATOR	";"
public static final String	FILTER_HEADER_START	"##FILTER"
public static final String	FORMAT_FIELD_SEPARATOR	":"
public static final String	FORMAT_HEADER_START	"##FORMAT"
public static final String	GENOTYPE_ALLELE_DEPTHS	"AD"
public static final String	GENOTYPE_FIELD_SEPARATOR	":"
public static final char	GENOTYPE_FIELD_SEPARATOR_CHAR	':'
public static final String	GENOTYPE_FILTER_KEY	"FT"
public static final String	GENOTYPE_KEY	"GT"
public static final String	GENOTYPE_LIKELIHOODS_KEY	"GL"
public static final String	GENOTYPE_PL_KEY	"PL"
public static final String	GENOTYPE_POSTERIORS_KEY	"GP"
public static final String	GENOTYPE_QUALITY_KEY	"GQ"
public static final String	HAPLOTYPE_QUALITY_KEY	"HQ"
public static final String	HAPMAP2_KEY	"H2"
public static final String	HAPMAP3_KEY	"H3"
public static final String	ID_FIELD_SEPARATOR	";"
public static final String	INFO_FIELD_ARRAY_SEPARATOR	","
public static final char	INFO_FIELD_ARRAY_SEPARATOR_CHAR	','
public static final String	INFO_FIELD_SEPARATOR	";"
public static final char	INFO_FIELD_SEPARATOR_CHAR	';'
public static final String	INFO_HEADER_START	"##INFO"
public static final char	INSERTION_ALLELE_v3	'I'
public static final String	MAPPING_QUALITY_ZERO_KEY	"MQ0"
public static final int	MAX_GENOTYPE_QUAL	99
public static final String	META_HEADER_KEY	"META"
public static final String	META_HEADER_START	"##META"
public static final String	MISSING_DEPTH_v3	"-1"
public static final String	MISSING_GENOTYPE_QUALITY_v3	"-1"
public static final String	MISSING_HAPLOTYPE_QUALITY_v3	"-1"
public static final String	MISSING_QUALITY_v3	"-1"
public static final String	MISSING_VALUE_v4	"."
public static final char	NO_CALL_ALLELE	'.'
public static final char	NULL_ALLELE	'-'
public static final String	OLD_DEPTH_KEY	"RD"
public static final String	PASSES_FILTERS_v3	"0"
public static final String	PASSES_FILTERS_v4	"PASS"
public static final String	PEDIGREE_HEADER_KEY	"PEDIGREE"
public static final String	PEDIGREE_HEADER_START	"##PEDIGREE"
public static final String	PER_ALLELE_COUNT	"R"
public static final String	PER_ALTERNATE_COUNT	"A"
public static final String	PER_GENOTYPE_COUNT	"G"
public static final String	PHASE_QUALITY_KEY	"PQ"
public static final String	PHASE_SET_KEY	"PS"
public static final String	PHASED	"|"
public static final String	PHASED_SWITCH_PROB_v3	"\\"
public static final String	PHASING_TOKENS	"/|\\"
public static final String	RMS_BASE_QUALITY_KEY	"BQ"
public static final String	RMS_MAPPING_QUALITY_KEY	"MQ"
public static final String	SAMPLE_HEADER_KEY	"SAMPLE"
public static final String	SAMPLE_HEADER_START	"##SAMPLE"
public static final String	SAMPLE_NUMBER_KEY	"NS"
public static final String	SOMATIC_KEY	"SOMATIC"
public static final char	SPANNING_DELETION_ALLELE	'*'
public static final String	STRAND_BIAS_KEY	"SB"
public static final String	SVTYPE	"SVTYPE"
public static final String	THOUSAND_GENOMES_KEY	"1000G"
public static final String	UNBOUNDED_ENCODING_v3	"-1"
public static final String	UNBOUNDED_ENCODING_v4	"."
public static final String	UNFILTERED	"."
public static final String	UNPHASED	"/"
public static final String	VALIDATED_KEY	"VALIDATED"

htsjdk.variant.vcf.VCFHeader

Modifier and Type	Constant Field	Value
public static final String	CONTIG_KEY	"contig"
public static final String	EXCLUDE_INTERVALS_KEY	"excludeIntervals"
public static final String	HEADER_INDICATOR	"#"
public static final String	INTERVAL_MERGING_KEY	"interval_merging"
public static final String	INTERVAL_PADDING_KEY	"interval_padding"
public static final String	INTERVAL_SET_RULE_KEY	"interval_set_rule"
public static final String	INTERVALS_KEY	"intervals"
public static final String	METADATA_INDICATOR	"##"
public static final String	REFERENCE_KEY	"reference"
public static final long	serialVersionUID	1L
public static final String	SOURCE_KEY	"source"

htsjdk.variant.vcf.VCFHeaderLine

Modifier and Type	Constant Field	Value
protected static final boolean	ALLOW_UNBOUND_DESCRIPTIONS	true
public static final long	serialVersionUID	1L
protected static final String	UNBOUND_DESCRIPTION	"Not provided in original VCF header"

htsjdk.variant.vcf.VCFSimpleHeaderLine

Modifier and Type	Constant Field	Value
public static final String	DESCRIPTION_ATTRIBUTE	"Description"
public static final String	ID_ATTRIBUTE	"ID"