Constant Field Values
Contents
net.sf.*
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net.sf.samtools.tabix.TabixIndex Modifier and Type Constant Field Value public static final int
TAD_LIDX_SHIFT
14
org.broad.*
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org.broad.igv.bbfile.BBFileHeader Modifier and Type Constant Field Value public static final int
BBFILE_HEADER_SIZE
64
public static final int
BIGBED_MAGIC_HTL
-336426617
public static final int
BIGBED_MAGIC_LTH
-2021002517
public static final int
BIGWIG_MAGIC_HTL
654085990
public static final int
BIGWIG_MAGIC_LTH
-2003829722
-
org.broad.igv.bbfile.BBFileReader Modifier and Type Constant Field Value public static final long
BBFILE_HEADER_OFFSET
0L
-
org.broad.igv.bbfile.BBTotalSummaryBlock Modifier and Type Constant Field Value public static final int
TOTAL_SUMMARY_BLOCK_SIZE
40
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org.broad.igv.bbfile.BBZoomLevelFormat Modifier and Type Constant Field Value public static final int
MAX_ZOOM_DATA_RECORDS
100000000
public static final int
ZOOM_FORMAT_HEADER_SIZE
4
-
org.broad.igv.bbfile.BBZoomLevelHeader Modifier and Type Constant Field Value public static final int
ZOOM_LEVEL_HEADER_SIZE
24
-
org.broad.igv.bbfile.BigWigSectionHeader Modifier and Type Constant Field Value public static final int
BEDGRAPH_ITEM_SIZE
12
public static final int
FIXEDSTEP_ITEM_SIZE
4
public static final int
SECTION_HEADER_SIZE
24
public static final int
VARSTEP_ITEM_SIZE
8
-
org.broad.igv.bbfile.BPTree Modifier and Type Constant Field Value public static final int
BPTREE_NODE_FORMAT_SIZE
4
public static final int
BPTREE_NODE_ITEM_SIZE
8
-
org.broad.igv.bbfile.BPTreeHeader Modifier and Type Constant Field Value public static final int
BPTREE_HEADER_SIZE
32
public static final int
BPTREE_MAGIC_HTL
-1853044104
public static final int
BPTREE_MAGIC_LTH
2026540177
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org.broad.igv.bbfile.RPTree Modifier and Type Constant Field Value public static final int
RPTREE_NODE_CHILD_ITEM_SIZE
24
public static final int
RPTREE_NODE_FORMAT_SIZE
4
public static final int
RPTREE_NODE_LEAF_ITEM_SIZE
32
-
org.broad.igv.bbfile.RPTreeHeader Modifier and Type Constant Field Value public final int
RPTREE_HEADER_SIZE
48
public final int
RPTREE_MAGIC_HTL
-525572060
public final int
RPTREE_MAGIC_LTH
610839776
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org.broad.igv.bbfile.ZoomDataRecord Modifier and Type Constant Field Value public static final int
RECORD_SIZE
32
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.Qseq2FastqSplit Modifier and Type Constant Field Value public static final int
SHOW_EVERY
100000
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org.snpeff.SnpEff Modifier and Type Constant Field Value public static final java.lang.String
BUILD
"2022-01-22 19:45"
public static final java.lang.String
BUILD_DATE
"2022-01-22 19:45"
public static final int
COMMAND_LINE_WIDTH
40
public static final java.lang.String
DEFAULT_COMMAND
"ann"
public static final java.lang.String
REVISION
"t"
public static final java.lang.String
SOFTWARE_NAME
"SnpEff"
public static final java.lang.String
VERSION
"SnpEff 4.3t (build 2022-01-22 19:45), by Pablo Cingolani"
public static final java.lang.String
VERSION_AUTHOR
"4.3t (build 2022-01-22 19:45), by Pablo Cingolani"
public static final java.lang.String
VERSION_BUILD
"4.3t (build 2022-01-22 19:45)"
public static final java.lang.String
VERSION_MAJOR
"4.3"
public static final java.lang.String
VERSION_SHORT
"4.3t"
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org.snpeff.akka.Master<TI,TO> Modifier and Type Constant Field Value public static final int
DEFAULT_BATCH_SIZE
10
public static final int
DEFAULT_SHOW_EVERY
1000
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org.snpeff.akka.msg.Work<T> Modifier and Type Constant Field Value public static final long
FIRST_SERIAL_NUMBER
1L
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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
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org.snpeff.align.VcfRefAltAlign Modifier and Type Constant Field Value public static final int
MAX_SIZE
10240
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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
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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
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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
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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
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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
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org.snpeff.codons.CodonTable Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_START_CODON
"M"
-
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"
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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
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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
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org.snpeff.fileIterator.LineClassFileIterator<T> Modifier and Type Constant Field Value public static final char
FIELD_NAME_SEPARATOR
59
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org.snpeff.fileIterator.MotifFileIterator Modifier and Type Constant Field Value public static final int
GFF_OFFSET
1
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org.snpeff.fileIterator.RegulationBedFileIterator Modifier and Type Constant Field Value public static final int
BED_OFFSET
0
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org.snpeff.fileIterator.RegulationGffFileIterator Modifier and Type Constant Field Value public static final int
GFF_OFFSET
1
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org.snpeff.fileIterator.TableFile Modifier and Type Constant Field Value protected static final char
FIELD_NAME_SEPARATOR
59
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org.snpeff.fileIterator.VcfFileIterator Modifier and Type Constant Field Value public static final java.lang.String
MISSING
"."
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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
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org.snpeff.genBank.Feature Modifier and Type Constant Field Value public static final java.lang.String
COMPLEMENT_STRING
"complement"
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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"
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org.snpeff.genBank.GenBank Modifier and Type Constant Field Value public static final int
FEATURE_NAME_FIELD_LEN
20
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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
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org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy Modifier and Type Constant Field Value public static final double
DEFAULT_MAX_PVALUE
0.05
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org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm Modifier and Type Constant Field Value public static final double
SCORE_CUTOFF_QUANTILE_DEFAULT
0.05
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org.snpeff.gsa.ScoreList Modifier and Type Constant Field Value public static final double
SIGNIFICANCE_LEVEL_95
0.05
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org.snpeff.gtex.Gtex Modifier and Type Constant Field Value public static final java.lang.String
NA_VALUE
"NA"
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org.snpeff.interval.CytoBands Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_CYTOBAND_BED_FILE
"cytoBand.txt.gz"
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org.snpeff.interval.ExonSpliceCharacterizer Modifier and Type Constant Field Value public static final int
MAX_EXONS
1000
public static final int
SHOW_EVERY
1000
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org.snpeff.interval.Gene Modifier and Type Constant Field Value public static final java.lang.String
CIRCULAR_GENE_ID
"_circ"
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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"
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org.snpeff.interval.Motif Modifier and Type Constant Field Value public static final boolean
debug
false
public static final double
SCORE_THRESHOLD
0.01
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org.snpeff.interval.ProteinInteractionLocus Modifier and Type Constant Field Value public static final boolean
debug
false
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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
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org.snpeff.interval.TranscriptSupportLevel Modifier and Type Constant Field Value public static final int
TSL_NULL_VALUE
9
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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
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org.snpeff.interval.codonChange.CodonChange Modifier and Type Constant Field Value public static final int
CODON_SIZE
3
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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
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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
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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
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org.snpeff.nextProt.NextProtDb Modifier and Type Constant Field Value public static final int
HIGHLY_CONSERVED_AA_COUNT
30
public static final double
HIGHLY_CONSERVED_AA_PERCENT
0.99
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org.snpeff.nextProt.NextProtParser Modifier and Type Constant Field Value public static final int
HIGHLY_CONSERVED_AA_COUNT
30
public static final double
HIGHLY_CONSERVED_AA_PERCENT
0.99
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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
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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
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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
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_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"
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org.snpeff.snpEffect.Hgvs Modifier and Type Constant Field Value public static final int
MAX_SEQUENCE_LEN_HGVS
100
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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"
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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
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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\">"
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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"
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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"
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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"
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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.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.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.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.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="