Constant Field Values

Contents

org.snpeff.*

  • org.snpeff.codons.CodonTable
    Modifier and Type
    Constant Field
    Value
    public static final String
    DEFAULT_START_CODON
    "M"
    public static final String
    TERMINATION_CODON
    "Ter"
    public static final String
    TERMINATION_CODON_1
    "*"
  • org.snpeff.codons.CodonTables
    Modifier and Type
    Constant Field
    Value
    public static final 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 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.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.gtex.Gtex
    Modifier and Type
    Constant Field
    Value
    public static final String
    NA_VALUE
    "NA"
  • org.snpeff.interval.codonChange.CodonChange
    Modifier and Type
    Constant Field
    Value
    public static final int
    CODON_SIZE
    3
  • org.snpeff.motif.Pwm
    Modifier and Type
    Constant Field
    Value
    public static final int
    SCALE
    100
  • org.snpeff.nmer.Nmer
    Modifier and Type
    Constant Field
    Value
    public static final int
    MAX_NMER_SIZE
    32
  • org.snpeff.reactome.events.Reaction
    Modifier and Type
    Constant Field
    Value
    public static final double
    MAX_WEIGHT_SUM
    1.1
  • 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
    '!'
    public static final byte
    GAP_CODE
    0xff
  • 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