Package org.snpeff.spliceSites

Class SnpEffCmdSpliceAnalysis

java.lang.Object
org.snpeff.SnpEff
org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
All Implemented Interfaces:
CommandLine
public class SnpEffCmdSpliceAnalysis extends SnpEff
Analyze sequences from splice sites
Author:
pcingola

  • Field Details

    • P_VALUE_THRESHOLD

      public static double P_VALUE_THRESHOLD

    • SIZE_CONSENSUS_DONOR

      public static int SIZE_CONSENSUS_DONOR

    • SIZE_CONSENSUS_ACCEPTOR

      public static int SIZE_CONSENSUS_ACCEPTOR

    • THRESHOLD_ENTROPY

      public static final double THRESHOLD_ENTROPY
      See Also:

    • THRESHOLD_COUNT

      public static final int THRESHOLD_COUNT
      See Also:

    • THRESHOLD_P

      public static final double THRESHOLD_P
      See Also:

    • THRESHOLD_BRANCH_U12_PERCENTILE

      public static final double THRESHOLD_BRANCH_U12_PERCENTILE
      See Also:

    • THRESHOLD_U12_OBSERVED_EXPECTED

      public static final double THRESHOLD_U12_OBSERVED_EXPECTED
      See Also:

    • HTML_WIDTH

      public static int HTML_WIDTH

    • HTML_HEIGHT

      public static int HTML_HEIGHT

  • Constructor Details

    • SnpEffCmdSpliceAnalysis

      public SnpEffCmdSpliceAnalysis()

  • Method Details

    • parseArgs

      public void parseArgs(String[] args)
      Description copied from class: SnpEff
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine
      Overrides:
      parseArgs in class SnpEff

    • run

      public boolean run()
      Description copied from class: SnpEff
      Run according to command line options
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • usage

      public void usage(String message)
      Description copied from class: SnpEff
      Show 'usage' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine
      Overrides:
      usage in class SnpEff