Constant Field Values

Contents

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

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 java.lang.String	BAM_FILE_EXTENSION	".bam"

htsjdk.samtools.BAMIndex

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAMIndexSuffix	".bai"

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.DownsamplingIteratorFactory

Modifier and Type	Constant Field	Value
public static final java.lang.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 >= 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead."
public static final java.lang.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 java.lang.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.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 java.lang.String	OC	"OC"
public static final java.lang.String	XF	"XF"
public static final java.lang.String	XN	"XN"
public static final java.lang.String	XQ	"XQ"
public static final java.lang.String	XS	"XS"
public static final java.lang.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 java.lang.String	CURRENT_VERSION	"1.5"
public static final java.lang.String	GROUP_ORDER_TAG	"GO"
public static final java.lang.String	SORT_ORDER_TAG	"SO"
public static final java.lang.String	VERSION_TAG	"VN"

htsjdk.samtools.SAMProgramRecord

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

htsjdk.samtools.SAMReadGroupRecord

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

htsjdk.samtools.SAMRecord

Modifier and Type	Constant Field	Value
public static final int	MAX_INSERT_SIZE	536870912
public static final java.lang.String	NO_ALIGNMENT_CIGAR	"*"
public static final int	NO_ALIGNMENT_REFERENCE_INDEX	-1
public static final java.lang.String	NO_ALIGNMENT_REFERENCE_NAME	"*"
public static final int	NO_ALIGNMENT_START	0
public static final int	NO_MAPPING_QUALITY	0
public static final java.lang.String	NULL_QUALS_STRING	"*"
public static final java.lang.String	NULL_SEQUENCE_STRING	"*"
public static final long	serialVersionUID	1L
public static final int	UNKNOWN_MAPPING_QUALITY	255

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 java.lang.String	ASSEMBLY_TAG	"AS"
public static final java.lang.String	MD5_TAG	"M5"
public static final java.lang.String	RESERVED_MRNM_SEQUENCE_NAME	"="
public static final java.lang.String	SEQUENCE_LENGTH_TAG	"LN"
public static final java.lang.String	SEQUENCE_NAME_TAG	"SN"
public static final long	serialVersionUID	1L
public static final java.lang.String	SPECIES_TAG	"SP"
public static final int	UNKNOWN_SEQUENCE_LENGTH	0
public static final java.lang.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.SQTagUtil

Modifier and Type	Constant Field	Value
public static final byte	MAX_QUALITY	63

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 java.lang.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 java.lang.String	CRAM_FILE_EXTENSION	".cram"

htsjdk.samtools.cram.build.Sam2CramRecordFactory

Modifier and Type	Constant Field	Value
public static final byte	ignorePositionsWithQualityScore	-1
public static final java.lang.String	UNKNOWN_READ_GROUP_ID	"UNKNOWN"
public static final java.lang.String	UNKNOWN_READ_GROUP_SAMPLE	"UNKNOWN"
public static final byte	unsetQualityScore	32

htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore

Modifier and Type	Constant Field	Value
public static final byte	operator	81

htsjdk.samtools.cram.encoding.readfeatures.Bases

Modifier and Type	Constant Field	Value
public static final byte	operator	98

htsjdk.samtools.cram.encoding.readfeatures.Deletion

Modifier and Type	Constant Field	Value
public static final byte	operator	68

htsjdk.samtools.cram.encoding.readfeatures.HardClip

Modifier and Type	Constant Field	Value
public static final byte	operator	72

htsjdk.samtools.cram.encoding.readfeatures.InsertBase

Modifier and Type	Constant Field	Value
public static final byte	operator	105

htsjdk.samtools.cram.encoding.readfeatures.Insertion

Modifier and Type	Constant Field	Value
public static final byte	operator	73

htsjdk.samtools.cram.encoding.readfeatures.Padding

Modifier and Type	Constant Field	Value
public static final byte	operator	80

htsjdk.samtools.cram.encoding.readfeatures.ReadBase

Modifier and Type	Constant Field	Value
public static final byte	operator	66

htsjdk.samtools.cram.encoding.readfeatures.RefSkip

Modifier and Type	Constant Field	Value
public static final byte	operator	78

htsjdk.samtools.cram.encoding.readfeatures.Scores

Modifier and Type	Constant Field	Value
public static final byte	operator	113

htsjdk.samtools.cram.encoding.readfeatures.SoftClip

Modifier and Type	Constant Field	Value
public static final byte	operator	83

htsjdk.samtools.cram.encoding.readfeatures.Substitution

Modifier and Type	Constant Field	Value
public static final int	NO_CODE	-1
public static final byte	operator	88

htsjdk.samtools.cram.ref.ReferenceTracks

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_WINDOW_SIZE	1000000

htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS

Modifier and Type	Constant Field	Value
public static final int	DUPLICATE_READ_FLAG	1024
public static final int	FIRST_OF_PAIR_FLAG	64
public static final int	MATE_STRAND_FLAG	32
public static final int	MATE_UNMAPPED_FLAG	8
public static final int	NOT_PRIMARY_ALIGNMENT_FLAG	256
public static final int	PROPER_PAIR_FLAG	2
public static final int	READ_FAILS_VENDOR_QUALITY_CHECK_FLAG	512
public static final int	READ_PAIRED_FLAG	1
public static final int	READ_STRAND_FLAG	16
public static final int	READ_UNMAPPED_FLAG	4
public static final int	SECOND_OF_PAIR_FLAG	128
public static final int	SUPPLEMENTARY_FLAG	2048

htsjdk.samtools.cram.structure.Slice

Modifier and Type	Constant Field	Value
public static final int	MULTI_REFERENCE	-2
public static final int	NO_ALIGNMENT_SPAN	0
public static final int	NO_ALIGNMENT_START	-1

htsjdk.samtools.fastq.FastqConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	QUALITY_HEADER	"+"
public static final java.lang.String	SEQUENCE_HEADER	"@"

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

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.Comparable>

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

htsjdk.samtools.seekablestream.SeekableBufferedStream

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

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 java.lang.String	CANNOT_SEEK_STREAM_MSG	"Cannot seek on stream based file "
public static final java.lang.String	INCORRECT_HEADER_SIZE_MSG	"Incorrect header size for file: "
public static final java.lang.String	INVALID_FILE_PTR_MSG	"Invalid file pointer: "
public static final java.lang.String	PREMATURE_END_MSG	"Premature end of file: "
public static final java.lang.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	66
public static final byte	BGZF_ID2	67
public static final byte	BGZF_LEN	2
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	8
public static final int	GZIP_FLG	4
public static final byte	GZIP_ID1	31
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.FormatUtil

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

htsjdk.samtools.util.IntervalList

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.String	DICT_FILE_EXTENSION	".dict"
public static final long	FIVE_GBS	5368709120L
public static final java.lang.String	INTERVAL_LIST_FILE_EXTENSION	".interval_list"
public static final long	ONE_GB	1073741824L
public static final java.lang.String	SAM_FILE_EXTENSION	".sam"
public static final long	TWO_GBS	2147483648L

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 java.lang.String	LAZY_NOW_LABEL	"NOW"

htsjdk.samtools.util.SequenceUtil

Modifier and Type	Constant Field	Value
public static final byte	a	97
public static final byte	A	65
public static final byte	c	99
public static final byte	C	67
public static final byte	g	103
public static final byte	G	71
public static final byte	n	110
public static final byte	N	78
public static final byte	t	116
public static final byte	T	84

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 java.lang.String	EMPTY_STRING	""

htsjdk.samtools.util.TestUtil

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

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 java.lang.String	STANDARD_INDEX_EXTENSION	".idx"

htsjdk.tribble.bed.BEDCodec

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

htsjdk.tribble.example.ExampleBinaryCodec

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

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.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 java.lang.String	STANDARD_INDEX_EXTENSION	".tbi"

htsjdk.variant.*

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 java.lang.String	NO_CALL_STRING	"."
public static final long	serialVersionUID	1L
public static final java.lang.String	SPAN_DEL_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 java.lang.String	PHASED_ALLELE_SEPARATOR	"|"
public static final long	serialVersionUID	1L
public static final java.lang.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 java.lang.String	VCF3_MAGIC_HEADER	"##fileformat=VCFv3"

htsjdk.variant.vcf.VCFCodec

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

htsjdk.variant.vcf.VCFConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_COUNT_KEY	"AC"
public static final java.lang.String	ALLELE_FREQUENCY_KEY	"AF"
public static final java.lang.String	ALLELE_NUMBER_KEY	"AN"
public static final java.lang.String	ALT_HEADER_START	"##ALT"
public static final java.lang.String	ANCESTRAL_ALLELE_KEY	"AA"
public static final java.lang.String	CIGAR_KEY	"CIGAR"
public static final java.lang.String	CONTIG_HEADER_KEY	"contig"
public static final java.lang.String	CONTIG_HEADER_START	"##contig"
public static final java.lang.String	DBSNP_KEY	"DB"
public static final char	DELETION_ALLELE_v3	68
public static final java.lang.String	DEPTH_KEY	"DP"
public static final java.lang.String	EMPTY_ALLELE	"."
public static final java.lang.String	EMPTY_ALTERNATE_ALLELE_FIELD	"."
public static final java.lang.String	EMPTY_GENOTYPE	"./."
public static final java.lang.String	EMPTY_ID_FIELD	"."
public static final java.lang.String	EMPTY_INFO_FIELD	"."
public static final java.lang.String	END_KEY	"END"
public static final java.lang.String	EXPECTED_ALLELE_COUNT_KEY	"EC"
public static final java.lang.String	FIELD_SEPARATOR	"\t"
public static final char	FIELD_SEPARATOR_CHAR	9
public static final java.lang.String	FILTER_CODE_SEPARATOR	";"
public static final java.lang.String	FILTER_HEADER_START	"##FILTER"
public static final java.lang.String	FORMAT_FIELD_SEPARATOR	":"
public static final java.lang.String	FORMAT_HEADER_START	"##FORMAT"
public static final java.lang.String	GENOTYPE_ALLELE_DEPTHS	"AD"
public static final java.lang.String	GENOTYPE_FIELD_SEPARATOR	":"
public static final char	GENOTYPE_FIELD_SEPARATOR_CHAR	58
public static final java.lang.String	GENOTYPE_FILTER_KEY	"FT"
public static final java.lang.String	GENOTYPE_KEY	"GT"
public static final java.lang.String	GENOTYPE_LIKELIHOODS_KEY	"GL"
public static final java.lang.String	GENOTYPE_PL_KEY	"PL"
public static final java.lang.String	GENOTYPE_POSTERIORS_KEY	"GP"
public static final java.lang.String	GENOTYPE_QUALITY_KEY	"GQ"
public static final java.lang.String	HAPLOTYPE_QUALITY_KEY	"HQ"
public static final java.lang.String	HAPMAP2_KEY	"H2"
public static final java.lang.String	HAPMAP3_KEY	"H3"
public static final java.lang.String	ID_FIELD_SEPARATOR	";"
public static final java.lang.String	INFO_FIELD_ARRAY_SEPARATOR	","
public static final char	INFO_FIELD_ARRAY_SEPARATOR_CHAR	44
public static final java.lang.String	INFO_FIELD_SEPARATOR	";"
public static final char	INFO_FIELD_SEPARATOR_CHAR	59
public static final java.lang.String	INFO_HEADER_START	"##INFO"
public static final char	INSERTION_ALLELE_v3	73
public static final java.lang.String	MAPPING_QUALITY_ZERO_KEY	"MQ0"
public static final int	MAX_GENOTYPE_QUAL	99
public static final java.lang.String	MISSING_DEPTH_v3	"-1"
public static final java.lang.String	MISSING_GENOTYPE_QUALITY_v3	"-1"
public static final java.lang.String	MISSING_HAPLOTYPE_QUALITY_v3	"-1"
public static final java.lang.String	MISSING_QUALITY_v3	"-1"
public static final java.lang.String	MISSING_VALUE_v4	"."
public static final char	NO_CALL_ALLELE	46
public static final char	NULL_ALLELE	45
public static final java.lang.String	OLD_DEPTH_KEY	"RD"
public static final java.lang.String	PASSES_FILTERS_v3	"0"
public static final java.lang.String	PASSES_FILTERS_v4	"PASS"
public static final java.lang.String	PER_ALLELE_COUNT	"R"
public static final java.lang.String	PER_ALTERNATE_COUNT	"A"
public static final java.lang.String	PER_GENOTYPE_COUNT	"G"
public static final java.lang.String	PHASE_QUALITY_KEY	"PQ"
public static final java.lang.String	PHASE_SET_KEY	"PS"
public static final java.lang.String	PHASED	"|"
public static final java.lang.String	PHASED_SWITCH_PROB_v3	"\\"
public static final java.lang.String	PHASING_TOKENS	"/|\\"
public static final java.lang.String	RMS_BASE_QUALITY_KEY	"BQ"
public static final java.lang.String	RMS_MAPPING_QUALITY_KEY	"MQ"
public static final java.lang.String	SAMPLE_NUMBER_KEY	"NS"
public static final java.lang.String	SOMATIC_KEY	"SOMATIC"
public static final char	SPANNING_DELETION_ALLELE	42
public static final java.lang.String	STRAND_BIAS_KEY	"SB"
public static final java.lang.String	SVTYPE	"SVTYPE"
public static final java.lang.String	THOUSAND_GENOMES_KEY	"1000G"
public static final java.lang.String	UNBOUNDED_ENCODING_v3	"-1"
public static final java.lang.String	UNBOUNDED_ENCODING_v4	"."
public static final java.lang.String	UNFILTERED	"."
public static final java.lang.String	UNPHASED	"/"
public static final java.lang.String	VALIDATED_KEY	"VALIDATED"

htsjdk.variant.vcf.VCFHeader

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONTIG_KEY	"contig"
public static final java.lang.String	EXCLUDE_INTERVALS_KEY	"excludeIntervals"
public static final java.lang.String	HEADER_INDICATOR	"#"
public static final java.lang.String	INTERVAL_MERGING_KEY	"interval_merging"
public static final java.lang.String	INTERVAL_PADDING_KEY	"interval_padding"
public static final java.lang.String	INTERVAL_SET_RULE_KEY	"interval_set_rule"
public static final java.lang.String	INTERVALS_KEY	"intervals"
public static final java.lang.String	METADATA_INDICATOR	"##"
public static final java.lang.String	REFERENCE_KEY	"reference"
public static final long	serialVersionUID	1L
public static final java.lang.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 java.lang.String	UNBOUND_DESCRIPTION	"Not provided in original VCF header"