Package 

Class TrimGenotypeTableAnchors

  • All Implemented Interfaces:
    
public class TrimGenotypeTableAnchors

    Simple class holding utilities to trim a genotype table by identity and coverage thresholds TODO needs to be refractored and have a standardized api Created by zrm22 on 7/6/17.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

      Constructors 
      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds) Method which will create a trimmed GenotypeTable based on the gene start and end positions
      static GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, String chr, int startPos, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds) Method which will create a trimmed GenotypeTable based on the gene start and end positions

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

    • Method Detail

      • createTrimmedFastaGenotypeTable

         static GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds)

        Method which will create a trimmed GenotypeTable based on the gene start and end positions

        Parameters:
        fastaFileName - Import fasta file to be read.
        refTaxaName - Name of the Reference taxa(ex B73Ref) which is a row in the fasta file.
        idThreshold - Percentage of Identity which needs to be met to be considered conserved.
        coverageThreshold - Percentage of Coverage across all lines in the fasta file which needs to be met to be considered conserved.
        leftTrimStart - Start point for the left direction trimming.
        rightTrimStart - Start point for the right direction trimming.
        consecFailingThresholds - Number of consecutive base pairs which need to fail to stop growing the region and start walking back to the gene bounds.
        consecPassingThresholds - Number of consecutive base pairs which need to pass the thresholds to stop shrinking the region and stop trimming.

      • createTrimmedFastaGenotypeTable

         static GenotypeTable createTrimmedFastaGenotypeTable(String fastaFileName, String refTaxaName, String chr, int startPos, double idThreshold, double coverageThreshold, int leftTrimStart, int rightTrimStart, int consecFailingThresholds, int consecPassingThresholds)

        Method which will create a trimmed GenotypeTable based on the gene start and end positions

        Parameters:
        fastaFileName - Import fasta file to be read.
        refTaxaName - Name of the Reference taxa(ex B73Ref) which is a row in the fasta file.
        chr - Name of the chromosome we need for the GenotypeTable
        startPos - Start position of the reference sequence so we can annotate the Position list
        idThreshold - Percentage of Identity which needs to be met to be considered conserved.
        coverageThreshold - Percentage of Coverage across all lines in the fasta file which needs to be met to be considered conserved.
        leftTrimStart - Start point for the left direction trimming.
        rightTrimStart - Start point for the right direction trimming.
        consecFailingThresholds - Number of consecutive base pairs which need to fail to stop growing the region and start walking back to the gene bounds.
        consecPassingThresholds - Number of consecutive base pairs which need to pass the thresholds to stop shrinking the region and stop trimming.