Package org.snpsift.fileIterator

Class DbNsfpEntry

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpsift.fileIterator.DbNsfpEntry
All Implemented Interfaces:
Serializable, Cloneable, Comparable<org.snpeff.interval.Interval>, org.snpeff.serializer.TxtSerializable
public class DbNsfpEntry extends org.snpeff.interval.Variant
DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs
Author:
lletourn
See Also:

  • Nested Class Summary

    Nested classes/interfaces inherited from class org.snpeff.interval.Variant

    org.snpeff.interval.Variant.VariantType

  • Field Summary

    Fields inherited from class org.snpeff.interval.Variant

    alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType

    Fields inherited from class org.snpeff.interval.Marker

    type

    Fields inherited from class org.snpeff.interval.Interval

    chromosomeNameOri, end, id, parent, start, strandMinus

  • Constructor Summary

    Constructors
    Constructor
    Description
    DbNsfpEntry(DbNsfp dbNsfp, String line)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    add(String columnName, String valuesToAdd)
    Add a value
    DbNsfpEntry
    cloneShallow()
     
    String
    getVcfInfo(String key)
    Get data in a VCF INFO field compatible format
    boolean
    hasValues(String allele)
    Do we have values for this allele
    protected void
    parseChrPosRefAlt()
    Parse dbSNFP 'Chr, pos, ref, alt' values from a single line
    protected void
    parseKeyValues()
    Parse dbSNFP ALL values from a single line and store them in 'values' hash
    int
    parsePosition(String posStr)
    Parse a string as a 'position'.
    static String[]
    splitValuesField(String value)
     
    String
    toString()
     

    Methods inherited from class org.snpeff.interval.Variant

    clone, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, realignLeft, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld

    Methods inherited from class org.snpeff.interval.Marker

    adjust, apply, applyDel, applyDup, applyIns, applyMixed, codonTable, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef

    Methods inherited from class org.snpeff.interval.Interval

    equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos

    Methods inherited from class java.lang.Object

    equals, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • DbNsfpEntry

      public DbNsfpEntry(DbNsfp dbNsfp, String line)

  • Method Details

    • splitValuesField

      public static String[] splitValuesField(String value)

    • add

      public void add(String columnName, String valuesToAdd)
      Add a value

    • cloneShallow

      public DbNsfpEntry cloneShallow()
      Overrides:
      cloneShallow in class org.snpeff.interval.Variant

    • getVcfInfo

      public String getVcfInfo(String key)
      Get data in a VCF INFO field compatible format

    • hasValues

      public boolean hasValues(String allele)
      Do we have values for this allele

    • parseChrPosRefAlt

      protected void parseChrPosRefAlt()
      Parse dbSNFP 'Chr, pos, ref, alt' values from a single line

    • parseKeyValues

      protected void parseKeyValues()
      Parse dbSNFP ALL values from a single line and store them in 'values' hash

      Note: This method is supposed to be a lazy parsing of the key/value pairs, so it DOES NOT store 'chr, pos, ref, alt'. You can use `parseChrPosRefAlt()` for that.

    • parsePosition

      public int parsePosition(String posStr)
      Parse a string as a 'position'.

    • toString

      public String toString()
      Overrides:
      toString in class org.snpeff.interval.Variant