Constant Field Values
Contents
htsjdk.samtools.*
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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"
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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"
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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
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htsjdk.samtools.Cigar Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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htsjdk.samtools.CigarElement Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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htsjdk.samtools.Defaults Modifier and Type Constant Field Value public static final String
DISABLE_SNAPPY_PROPERTY_NAME
"snappy.disable"
public static final String
SAMJDK_PREFIX
"samjdk."
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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."
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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
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htsjdk.samtools.LinearIndex Modifier and Type Constant Field Value public static final int
BAM_LIDX_SHIFT
14
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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"
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htsjdk.samtools.SAMBinaryTagAndValue Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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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"
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htsjdk.samtools.SamFileValidator Modifier and Type Constant Field Value public static final int
MAX_QUALITY_NOT_STORED_ERRORS
100
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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"
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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"
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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
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htsjdk.samtools.SAMRecordSetBuilder Modifier and Type Constant Field Value public static final int
DEFAULT_CHROMOSOME_LENGTH
200000000
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htsjdk.samtools.SAMSequenceDictionary Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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htsjdk.samtools.SAMSequenceRecord Modifier and Type Constant Field Value 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"
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htsjdk.samtools.SAMUtils Modifier and Type Constant Field Value public static final int
MAX_PHRED_SCORE
93
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htsjdk.samtools.SAMValidationError Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
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htsjdk.samtools.SBIIndex Modifier and Type Constant Field Value public static final String
FILE_EXTENSION
".sbi"
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htsjdk.samtools.SBIIndexWriter Modifier and Type Constant Field Value public static final long
DEFAULT_GRANULARITY
4096L
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htsjdk.samtools.SQTagUtil Modifier and Type Constant Field Value public static final byte
MAX_QUALITY
63
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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
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htsjdk.samtools.cram.CRAIIndex Modifier and Type Constant Field Value public static final String
CRAI_INDEX_SUFFIX
".crai"
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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
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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
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htsjdk.samtools.cram.compression.ExternalCompressor Modifier and Type Constant Field Value public static final int
NO_COMPRESSION_ARG
-1
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htsjdk.samtools.cram.compression.rans.RANS Modifier and Type Constant Field Value public static final int
NUMBER_OF_SYMBOLS
256
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htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore Modifier and Type Constant Field Value public static final byte
operator
81
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htsjdk.samtools.cram.encoding.readfeatures.Bases Modifier and Type Constant Field Value public static final byte
operator
98
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htsjdk.samtools.cram.encoding.readfeatures.Deletion Modifier and Type Constant Field Value public static final byte
operator
68
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htsjdk.samtools.cram.encoding.readfeatures.HardClip Modifier and Type Constant Field Value public static final byte
operator
72
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htsjdk.samtools.cram.encoding.readfeatures.InsertBase Modifier and Type Constant Field Value public static final byte
operator
105
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htsjdk.samtools.cram.encoding.readfeatures.Insertion Modifier and Type Constant Field Value public static final byte
operator
73
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htsjdk.samtools.cram.encoding.readfeatures.Padding Modifier and Type Constant Field Value public static final byte
operator
80
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htsjdk.samtools.cram.encoding.readfeatures.ReadBase Modifier and Type Constant Field Value public static final byte
operator
66
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htsjdk.samtools.cram.encoding.readfeatures.RefSkip Modifier and Type Constant Field Value public static final byte
operator
78
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htsjdk.samtools.cram.encoding.readfeatures.Scores Modifier and Type Constant Field Value public static final byte
operator
113
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htsjdk.samtools.cram.encoding.readfeatures.SoftClip Modifier and Type Constant Field Value public static final byte
operator
83
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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
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htsjdk.samtools.cram.io.ITF8 Modifier and Type Constant Field Value public static final int
MAX_BYTES
5
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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
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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
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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
-1
public static final int
NO_READGROUP_ID
-1
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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
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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
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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
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htsjdk.samtools.cram.structure.block.Block Modifier and Type Constant Field Value public static final int
NO_CONTENT_ID
0
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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
"@"
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htsjdk.samtools.filter.AbstractJavascriptFilter<HEADER,TYPE> Modifier and Type Constant Field Value public static final String
DEFAULT_HEADER_KEY
"header"
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htsjdk.samtools.liftover.LiftOver Modifier and Type Constant Field Value public static final double
DEFAULT_LIFTOVER_MINMATCH
0.95
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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"
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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
32
public static final char
HEADER_START_CHAR
62
-
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
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htsjdk.samtools.sra.SRAUtils Modifier and Type Constant Field Value public static final int
REFERENCE_ALIGNMENT
5000
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htsjdk.samtools.util.AbstractAsyncWriter<T> Modifier and Type Constant Field Value public static final int
DEFAULT_QUEUE_SIZE
2000
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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
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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
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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: "
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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
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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
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"
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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
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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
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 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.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 char
ATTRIBUTE_DELIMITER
59
public static final String
COMMENT_START
"#"
public static final String
DIRECTIVE_START
"##"
public static final char
END_OF_LINE_CHARACTER
10
public static final char
FIELD_DELIMITER
9
public static final char
KEY_VALUE_SEPARATOR
61
public static final String
PARENT_ATTRIBUTE_KEY
"Parent"
public static final String
UNDEFINED_FIELD_VALUE
"."
public static final char
VALUE_DELIMITER
44
-
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 String
NO_CALL_STRING
"."
public static final String
NON_REF_STRING
"<NON_REF>"
public static final long
serialVersionUID
1L
public static final String
SPAN_DEL_STRING
"*"
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
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htsjdk.variant.vcf.AbstractVCFCodec Modifier and Type Constant Field Value protected static final int
NUM_STANDARD_FIELDS
8
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htsjdk.variant.vcf.VCF3Codec Modifier and Type Constant Field Value public static final String
VCF3_MAGIC_HEADER
"##fileformat=VCFv3"
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htsjdk.variant.vcf.VCFCodec Modifier and Type Constant Field Value public static final String
VCF4_MAGIC_HEADER
"##fileformat=VCFv4"
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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
68
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
9
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
58
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
44
public static final String
INFO_FIELD_SEPARATOR
";"
public static final char
INFO_FIELD_SEPARATOR_CHAR
59
public static final String
INFO_HEADER_START
"##INFO"
public static final char
INSERTION_ALLELE_v3
73
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
46
public static final char
NULL_ALLELE
45
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
42
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"
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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"
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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"
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htsjdk.variant.vcf.VCFSimpleHeaderLine Modifier and Type Constant Field Value public static final String
DESCRIPTION_ATTRIBUTE
"Description"
public static final String
ID_ATTRIBUTE
"ID"