Constant Field Values

Contents

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.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.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.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.gtex.Gtex 
    Modifier and Type Constant Field Value
    public static final java.lang.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.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.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