Constant Field Values

Contents

• org.snpeff.*

org.snpeff.*

org.snpeff.Fastq2Fastq

Modifier and Type	Constant Field	Value
public static final int	SHOW_EVERY	100000

org.snpeff.Pcingola

Modifier and Type	Constant Field	Value
public static final java.lang.String	BY	"Pablo Cingolani"
public static final java.lang.String	EMAIL	"pcingola@users.sourceforge.net"

org.snpeff.Qseq2Fastq

Modifier and Type	Constant Field	Value
public static final int	SHOW_EVERY	100000

org.snpeff.SnpEff

Modifier and Type	Constant Field	Value
public static final java.lang.String	BUILD	"2022-02-24 06:09"
public static final java.lang.String	BUILD_DATE	"2022-02-24 06:09"
public static final int	COMMAND_LINE_WIDTH	40
public static final java.lang.String	DEFAULT_COMMAND	"ann"
public static final java.lang.String	REVISION	""
public static final java.lang.String	SOFTWARE_NAME	"SnpEff"
public static final java.lang.String	VERSION	"SnpEff 5.1 (build 2022-02-24 06:09), by Pablo Cingolani"
public static final java.lang.String	VERSION_AUTHOR	"5.1 (build 2022-02-24 06:09), by Pablo Cingolani"
public static final java.lang.String	VERSION_BUILD	"5.1 (build 2022-02-24 06:09)"
public static final java.lang.String	VERSION_MAJOR	"5.1"
public static final java.lang.String	VERSION_SHORT	"5.1"

org.snpeff.align.VariantRealign

Modifier and Type	Constant Field	Value
public static final int	INITIAL_BASES_EXTRA	10
public static final int	INITIAL_BASES_MULTIPLIER	3
public static final int	MAX_ITERATIONS	100
public static final int	PROGRESSIVE_BASES_EXTRA	1
public static final int	PROGRESSIVE_BASES_MULTIPLIER	2

org.snpeff.align.VcfRefAltAlign

Modifier and Type	Constant Field	Value
public static final int	MAX_SIZE	10240

org.snpeff.binseq.DnaSequenceByte

Modifier and Type	Constant Field	Value
public static final int	BASES_PER_BYTE	4
public static final int	BITS_PER_BASE	2

org.snpeff.binseq.GenomicSequences

Modifier and Type	Constant Field	Value
public static final int	CHR_LEN_SEPARATE_FILE	1000000
public static final int	MAX_ITERATIONS	1000000

org.snpeff.binseq.coder.Coder

Modifier and Type	Constant Field	Value
public static final int	BITS_PER_LONGWORD	64
public static final int	BYTES_PER_LONGWORD	8

org.snpeff.binseq.coder.DnaCoder

Modifier and Type	Constant Field	Value
protected static final int	BASES_PER_LONGWORD	32
protected static final int	BITS_PER_BASE	2
protected static final int	LAST_BASE_IN_LONGWORD	31
public static final long	MASK_ALL_WORD	-1L
protected static final long	MASK_FIRST_BASE	3L

org.snpeff.binseq.coder.DnaQualityCoder

Modifier and Type	Constant Field	Value
public static final int	MAX_QUALITY	63
public static final int	MIN_QUALITY	0

org.snpeff.codons.CodonTable

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_START_CODON	"M"
public static final java.lang.String	TERMINATION_CODON	"Ter"
public static final java.lang.String	TERMINATION_CODON_1	"*"

org.snpeff.codons.CodonTables

Modifier and Type	Constant Field	Value
public static final java.lang.String	STANDARD_TABLE	"TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G"
public static final java.lang.String	STANDARD_TABLE_NAME	"Standard"

org.snpeff.codons.FindRareAaIntervals

Modifier and Type	Constant Field	Value
public static final double	RARE_THRESHOLD	1.0E-5

org.snpeff.collections.HashLongLongArray

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

org.snpeff.coverage.CountReadsOnMarkers

Modifier and Type	Constant Field	Value
public static final int	MAX_EXONS_CHART	10
public static final int	SHOW_EVERY	10000

org.snpeff.fastq.FastqSplit

Modifier and Type	Constant Field	Value
public static final int	BUFFER_SIZE	10485760
public static final long	G	1073741824L
public static final long	K	1024L
public static final long	M	1048576L
public static final long	P	1125899906842624L
public static final long	T	1099511627776L

org.snpeff.fileIterator.LineClassFileIterator<T>

Modifier and Type	Constant Field	Value
public static final char	FIELD_NAME_SEPARATOR	59

org.snpeff.fileIterator.MotifFileIterator

Modifier and Type	Constant Field	Value
public static final int	GFF_OFFSET	1

org.snpeff.fileIterator.RegulationBedFileIterator

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

org.snpeff.fileIterator.RegulationGffFileIterator

Modifier and Type	Constant Field	Value
public static final int	GFF_OFFSET	1

org.snpeff.fileIterator.TableFile

Modifier and Type	Constant Field	Value
protected static final char	FIELD_NAME_SEPARATOR	59

org.snpeff.fileIterator.VcfFileIterator

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

org.snpeff.genBank.Embl

Modifier and Type	Constant Field	Value
public static final int	FEATURE_KEY_LEN	5
public static final int	FEATURE_NAME_LEN	15

org.snpeff.genBank.Feature

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMPLEMENT_STRING	"complement"

org.snpeff.genBank.Features

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMPLEMENT	"complement"
public static final java.lang.String	JOIN	"join"
public static final int	MAX_LEN_TO_SHOW	200
public static final java.lang.String	ORDER	"order"

org.snpeff.genBank.GenBank

Modifier and Type	Constant Field	Value
public static final int	FEATURE_NAME_FIELD_LEN	20

org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

Modifier and Type	Constant Field	Value
public static final java.lang.String	HTML_BG_COLOR_TITLE	"cccccc"
public static final int	HTML_TD_GENES_MAX_LEN	40

org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MAX_PVALUE	0.05

org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm

Modifier and Type	Constant Field	Value
public static final double	SCORE_CUTOFF_QUANTILE_DEFAULT	0.05

org.snpeff.gsa.ScoreList

Modifier and Type	Constant Field	Value
public static final double	SIGNIFICANCE_LEVEL_95	0.05

org.snpeff.gtex.Gtex

Modifier and Type	Constant Field	Value
public static final java.lang.String	NA_VALUE	"NA"

org.snpeff.interval.CytoBands

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CYTOBAND_BED_FILE	"cytoBand.txt.gz"

org.snpeff.interval.ExonSpliceCharacterizer

Modifier and Type	Constant Field	Value
public static final int	MAX_EXONS	1000
public static final int	SHOW_EVERY	1000

org.snpeff.interval.Gene

Modifier and Type	Constant Field	Value
public static final java.lang.String	CIRCULAR_GENE_ID	"_circ"

org.snpeff.interval.Intergenic

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHROMOSOME_END	"CHR_END"
public static final java.lang.String	CHROMOSOME_START	"CHR_START"

org.snpeff.interval.Motif

Modifier and Type	Constant Field	Value
public static final boolean	debug	false
public static final double	SCORE_THRESHOLD	0.01

org.snpeff.interval.ProteinInteractionLocus

Modifier and Type	Constant Field	Value
public static final boolean	debug	false

org.snpeff.interval.SpliceSite

Modifier and Type	Constant Field	Value
public static final int	CORE_SPLICE_SITE_SIZE	2
public static final int	SPLICE_REGION_EXON_SIZE	3
public static final int	SPLICE_REGION_INTRON_MAX	8
public static final int	SPLICE_REGION_INTRON_MIN	3

org.snpeff.interval.TranscriptSupportLevel

Modifier and Type	Constant Field	Value
public static final int	TSL_NULL_VALUE	9

org.snpeff.interval.Variant

Modifier and Type	Constant Field	Value
public static final double	HUGE_DELETION_RATIO_THRESHOLD	0.01
public static final int	HUGE_DELETION_SIZE_THRESHOLD	1000000

org.snpeff.interval.codonChange.CodonChange

Modifier and Type	Constant Field	Value
public static final int	CODON_SIZE	3

org.snpeff.interval.tree.IntervalTreeArray

Modifier and Type	Constant Field	Value
public static final int	INITIAL_CAPACITY	1024
public static final int	MIN_MARKERS_PER_LEAF	4

org.snpeff.logStatsServer.LogStats

Modifier and Type	Constant Field	Value
public static final int	LOG_THREAD_WAIT_TIME	1000
public static final int	LOG_THREAD_WAIT_TIME_REPEAT	5

org.snpeff.logStatsServer.VersionCheck

Modifier and Type	Constant Field	Value
public static final int	LOG_THREAD_WAIT_TIME	1000
public static final int	LOG_THREAD_WAIT_TIME_REPEAT	3

org.snpeff.motif.Pwm

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

org.snpeff.nextProt.NextProtSequenceConservation

Modifier and Type	Constant Field	Value
public static final int	HIGHLY_CONSERVED_AA_COUNT	5
public static final double	HIGHLY_CONSERVED_AA_PERCENT	0.99

org.snpeff.nmer.Nmer

Modifier and Type	Constant Field	Value
public static final int	MAX_NMER_SIZE	32

org.snpeff.outputFormatter.VcfOutputFormatter

Modifier and Type	Constant Field	Value
public static final java.lang.String	VCF_INFO_OICR_NAME	"OICR"

org.snpeff.ped.TfamEntry

Modifier and Type	Constant Field	Value
public static final int	PHENOTYPE_CASE	2
public static final int	PHENOTYPE_CONTROL	1
public static final int	PHENOTYPE_MISSING	-9

org.snpeff.probablility.NormalDistribution

Modifier and Type	Constant Field	Value
public static final double	MAX_NORM_DOUBLE	700.0

org.snpeff.probablility.RankSumPdf

Modifier and Type	Constant Field	Value
public static final int	CACHE_MAX_N	40
public static final int	CACHE_MAX_NT	40

org.snpeff.reactome.Reactome

Modifier and Type	Constant Field	Value
public static final double	EPSILON	1.0E-6
public static final double	MAX_CONVERGENCE_DIFFERENCE	0.001
public static final int	MAX_ITERATIONS	1000
public static final int	SHOW_EVERY	10000

org.snpeff.reactome.events.Reaction

Modifier and Type	Constant Field	Value
public static final double	MAX_WEIGHT_SUM	1.1

org.snpeff.snpEffect.Config

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONFIG_FILE	"snpEff.config"
public static final java.lang.String	DEFAULT_DATA_DIR	"./data"
public static final java.lang.String	ETC_CONFIG_FILE	"/etc/snpeff/snpEff.config"
public static final java.lang.String	KEY_BUNDLE_SUFIX	".bundle"
public static final java.lang.String	KEY_CODON_PREFIX	"codon."
public static final java.lang.String	KEY_CODONTABLE_SUFIX	".codonTable"
public static final java.lang.String	KEY_COORDINATES	"coordinates"
public static final java.lang.String	KEY_DATA_DIR	"data.dir"
public static final java.lang.String	KEY_DATABASE_LOCAL	"database"
public static final java.lang.String	KEY_DATABASE_REPOSITORY	"database.repository"
public static final java.lang.String	KEY_DATABASE_REPOSITORY_KEY	"database.repositoryKey"
public static final java.lang.String	KEY_DBNSFP_FIELDS	"dbnsfp.fields"
public static final java.lang.String	KEY_GENOME_SUFIX	".genome"
public static final java.lang.String	KEY_LOF_DELETE_PROTEIN_CODING_BASES	"lof.deleteProteinCodingBases"
public static final java.lang.String	KEY_LOF_IGNORE_PROTEIN_CODING_AFTER	"lof.ignoreProteinCodingAfter"
public static final java.lang.String	KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE	"lof.ignoreProteinCodingBefore"
public static final java.lang.String	KEY_REFERENCE_SUFIX	".reference"
public static final java.lang.String	KEY_VERSIONS_URL	"versions.url"

org.snpeff.snpEffect.Hgvs

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

org.snpeff.snpEffect.LossOfFunction

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_DELETE_PROTEIN_CODING_BASES	0.5
public static final double	DEFAULT_IGNORE_PROTEIN_CODING_AFTER	0.95
public static final double	DEFAULT_IGNORE_PROTEIN_CODING_BEFORE	0.05
public static final int	MND_BASES_BEFORE_LAST_JUNCTION	50
public static final java.lang.String	VCF_INFO_LOF_NAME	"LOF"
public static final java.lang.String	VCF_INFO_NMD_NAME	"NMD"

org.snpeff.snpEffect.PurityChange

Modifier and Type	Constant Field	Value
public static final int	CODONS_AROUND	5
public static final int	CODONS_SIZE	3
public static final boolean	debug	false
public static final java.lang.String	KEY_SEPARATOR	"\t"
public static final int	MIN_COUNT_CODON	2

org.snpeff.snpEffect.SnpEffectPredictor

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_UP_DOWN_LENGTH	5000
public static final int	SMALL_VARIANT_SIZE_THRESHOLD	10

org.snpeff.snpEffect.VariantEffect

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

org.snpeff.snpEffect.commandLine.SnpEffCmdAcat

Modifier and Type	Constant Field	Value
public static final java.lang.String	ACAT	"ACAT"
public static final double	CONSERVATION_THRESHOLD	0.99
public static final java.lang.String	NCACTIVITY	"NCACTIVITY"
public static final java.lang.String	NCCAT	"NCCAT"
public static final java.lang.String	NCCONS	"NCCONS"
public static final java.lang.String	NCELEMENT	"NCELEMENT"
public static final java.lang.String	NCFACTOR	"NCFACTOR"
public static final java.lang.String	NCMARK	"NCMARK"
public static final java.lang.String	T2D_GENES	"T2D_GENES"

org.snpeff.snpEffect.commandLine.SnpEffCmdClosest

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLOSEST	"CLOSEST"
public static final java.lang.String	INFO_LINE	"##INFO=<ID=CLOSEST,Number=4,Type=String,Description=\"Closest exon: Distance (bases), exons Id, transcript Id, gene name\">"

org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases

Modifier and Type	Constant Field	Value
public static final java.lang.String	DARK_ROW	"bgcolor=#CCCCCC"
public static final java.lang.String	FTP_PROTOCOL	"ftp://"
public static final java.lang.String	HTTP_PROTOCOL	"http://"
public static final java.lang.String	LIGHT_ROW	"bgcolor=#EEEEEE"

org.snpeff.snpEffect.commandLine.SnpEffCmdEff

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_SUMMARY_CSV_FILE	"snpEff_summary.csv"
public static final java.lang.String	DEFAULT_SUMMARY_GENES_FILE	"snpEff_genes.txt"
public static final java.lang.String	DEFAULT_SUMMARY_HTML_FILE	"snpEff_summary.html"
public static final int	SHOW_EVERY	10000
public static final java.lang.String	SUMMARY_CSV_TEMPLATE	"snpEff_csv_summary.ftl"
public static final java.lang.String	SUMMARY_GENES_TEMPLATE	"snpEff_genes.ftl"
public static final java.lang.String	SUMMARY_TEMPLATE	"snpEff_summary.ftl"
public static final java.lang.String	TEMPLATES_DIR	"src/main/resources"

org.snpeff.snpEffect.commandLine.SnpEffCmdPdb

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_DISTANCE_THRESHOLD	3.0
public static final java.lang.String	DEFAULT_ID_MAP_FILE	"db/pdb/idMap_pdbId_ensemblId_refseqId.txt.gz"
public static final java.lang.String	DEFAULT_INTERACT_FILE	"db/pdb/pdbCompoundLines.txt"
public static final double	DEFAULT_MAX_MISMATCH_RATE	0.1
public static final java.lang.String	DEFAULT_PDB_DIR	"db/pdb"
public static final int	DEFAULT_PDB_MIN_AA_SEPARATION	20
public static final java.lang.String	DEFAULT_PDB_ORGANISM_COMMON	"HUMAN"
public static final java.lang.String	DEFAULT_PDB_ORGANISM_SCIENTIFIC	"HOMO SAPIENS"
public static final double	DEFAULT_PDB_RESOLUTION	3.0
public static final java.lang.String	PDB_EXT	".ent"
public static final java.lang.String	PDB_EXT_GZ	".ent.gz"
public static final java.lang.String	PROTEIN_INTERACTION_FILE	"interactions.bin"
public static final java.lang.String	UNIPROT_DATABASE	"UNP"

org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_REPORT_HTML_FILE	"translocations_report.html"
public static final java.lang.String	REPORT_TEMPLATE	"translocations_report.ftl"

org.snpeff.snpEffect.factory.SnpEffPredictorFactory

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

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXTENSION_EMBL	".embl"

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures

Modifier and Type	Constant Field	Value
public static final int	OFFSET	1

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXTENSION_GENBANK	".gbk"

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff

Modifier and Type	Constant Field	Value
public static final java.lang.String	FASTA_DELIMITER	"##FASTA"

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene

Modifier and Type	Constant Field	Value
public static final java.lang.String	CDS_STAT_COMPLETE	"cmpl"

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq

Modifier and Type	Constant Field	Value
public static final java.lang.String	CDS_STAT_COMPLETE	"cmpl"

org.snpeff.snpEffect.testCases.integration.IntegrationTest

Modifier and Type	Constant Field	Value
public final int	BUFFER_SIZE	10485760
public static final int	MAX_LINES_DIFF	20

org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase

Modifier and Type	Constant Field	Value
public static final java.lang.String	BASE_DIR	"tests"

org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCutsomIntervals

Modifier and Type	Constant Field	Value
public static final int	NUM_DEL_TEST	10

org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof

Modifier and Type	Constant Field	Value
public static final int	NUM_DEL_TEST	10

org.snpeff.snpEffect.testCases.unity.TestCasesBase

Modifier and Type	Constant Field	Value
public static final java.lang.String	BASE_DIR	"tests"

org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList

Modifier and Type	Constant Field	Value
public static final double	EPSILON	1.0E-10

org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer

Modifier and Type	Constant Field	Value
public static final int	NMER_SIZE	15

org.snpeff.spliceSites.AcgtTree

Modifier and Type	Constant Field	Value
public static final int	FAKE_COUNTS	1
public static final double	MAX_ENTROPY	2.0

org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis

Modifier and Type	Constant Field	Value
public static final double	THRESHOLD_BRANCH_U12_PERCENTILE	0.95
public static final int	THRESHOLD_COUNT	100
public static final double	THRESHOLD_ENTROPY	0.05
public static final double	THRESHOLD_P	0.95
public static final double	THRESHOLD_U12_OBSERVED_EXPECTED	5.0

org.snpeff.spliceSites.SpliceTypes

Modifier and Type	Constant Field	Value
public static final int	THRESHOLD_COUNT	100
public static final double	THRESHOLD_ENTROPY	0.05
public static final double	THRESHOLD_P	0.95

org.snpeff.spliceSites.TranscriptSet

Modifier and Type	Constant Field	Value
public static final int	MAX_TRANSCRIPTS_PER_GENE	1000

org.snpeff.stats.AlleleCountStats

Modifier and Type	Constant Field	Value
public static final int	MAX_MAC	1000

org.snpeff.stats.CountByType

Modifier and Type	Constant Field	Value
public static final java.lang.String	TOTAL_TYPE	"Total"

org.snpeff.stats.PosStats

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BINS	101

org.snpeff.stats.VariantEffectStats

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHANGE_SEPARATOR	"\t"

org.snpeff.stats.VariantStats

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHANGE_SEPARATOR	"\t"

org.snpeff.stats.VariantTypeStats

Modifier and Type	Constant Field	Value
public static final int	MAX_MAC	1000

org.snpeff.stats.plot.GooglePlot

Modifier and Type	Constant Field	Value
public static final int	MAX_DATA_POINTS	300

org.snpeff.stats.plot.GooglePlotInt

Modifier and Type	Constant Field	Value
public static final int	MAX_DATA_POINTS	300

org.snpeff.svg.Svg

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BASE_Y	10
public static final int	DEFAULT_SIZE_X	1000
public static final int	DEFAULT_SIZE_Y	1000
public static final java.lang.String	LINE_COLOR_STROKE	"#000000"
public static final int	LINE_STROKE_WIDTH	1
public static final java.lang.String	RECT_COLOR_FILL	"#FFFFFF"
public static final java.lang.String	RECT_COLOR_STROKE	"#000000"
public static final int	RECT_HEIGHT	20
public static final int	RECT_STROKE_WIDTH	1
public static final int	TEXT_SIZE	10
public static final java.lang.String	TEXT_STYLE	"font-family: Arial; font-size:10;"

org.snpeff.svg.SvgBnd

Modifier and Type	Constant Field	Value
public static final int	BND_CURL_SIZE	50

org.snpeff.svg.SvgIntron

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

org.snpeff.svg.SvgScale

Modifier and Type	Constant Field	Value
public static final int	SCALE_HEIGHT	30
public static final int	SCALE_TICK_HEIGHT	20

org.snpeff.util.Download

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PROXY_PORT	80

org.snpeff.util.Gpr

Modifier and Type	Constant Field	Value
public static final long	GB	1073741824L
public static final long	KB	1024L
public static final long	MB	1048576L
public static final long	TB	1099511627776L

org.snpeff.util.GprSeq

Modifier and Type	Constant Field	Value
public static final char	FASTQ_SANGER_ZERO	33
public static final byte	GAP_CODE	-1

org.snpeff.util.IubString

Modifier and Type	Constant Field	Value
public static final int	MAX_IUB_BASES	10

org.snpeff.util.Log

Modifier and Type	Constant Field	Value
public static final int	MAX_ERRORS	10
public static final int	MAX_WARNINGS	25

org.snpeff.vcf.EffFormatVersion

Modifier and Type	Constant Field	Value
public static final java.lang.String	EFFECT_TYPE_SEPARATOR	"&"
public static final java.lang.String	EFFECT_TYPE_SEPARATOR_OLD	"+"
public static final java.lang.String	VCF_INFO_ANN_NAME	"ANN"
public static final java.lang.String	VCF_INFO_EFF_NAME	"EFF"

org.snpeff.vcf.FileIndexChrPos

Modifier and Type	Constant Field	Value
public static final int	POS_OFFSET	1

org.snpeff.vcf.VcfConsequence

Modifier and Type	Constant Field	Value
public static final java.lang.String	VCF_INFO_CSQ_NAME	"CSQ"

org.snpeff.vcf.VcfEntry

Modifier and Type	Constant Field	Value
public static final double	ALLELE_FEQUENCY_COMMON	0.05
public static final double	ALLELE_FEQUENCY_LOW	0.01
public static final java.lang.String	FILTER_PASS	"PASS"
public static final java.lang.String	SUB_FIELD_SEP	";"
public static final java.lang.String	VCF_ALT_MISSING_REF	"*"
public static final java.lang.String	VCF_ALT_NON_REF	"<*>"
public static final java.lang.String	VCF_ALT_NON_REF_gVCF	"<NON_REF>"
public static final java.lang.String	VCF_INFO_END	"END"
public static final java.lang.String	VCF_INFO_HETS	"HE"
public static final java.lang.String	VCF_INFO_HOMS	"HO"
public static final java.lang.String	VCF_INFO_NAS	"NA"
public static final java.lang.String	VCF_INFO_PRIVATE	"Private"
public static final char	WITHIN_FIELD_SEP	44

org.snpeff.vcf.VcfGenotype

Modifier and Type	Constant Field	Value
public static final java.lang.String	GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE	"AD"
public static final java.lang.String	GT_FIELD_DEPTH_OF_COVERAGE	"DP"

org.snpeff.vcf.VcfHeader

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHROM_PREFIX	"#CHROM\t"
public static final java.lang.String	FORMAT_PREFIX	"##FORMAT="
public static final java.lang.String	INFO_PREFIX	"##INFO="
public static final java.lang.String	PEDIGREE_PREFIX	"##PEDIGREE="