Constructor Detail

Method Detail

• checkChrom2DupAnchor

   static void checkChrom2DupAnchor(String refGenome)

• calcLevenshtein

   static int calcLevenshtein(String seq1, String seq2, int maxEditDistance)

• testPythonLD

   static void testPythonLD(String seq1, String seq2, String mode, String task)

• printTrimTables

   static void printTrimTables(String origData, String trimData, String outputFile)

• freqChartHaplotypeCollapse

   static void freqChartHaplotypeCollapse(String inputFile, String outputDir)

• freqHaplotypeCollapse

   static void freqHaplotypeCollapse(String inputFile, String outputDir)

• testMafftfromJava

   static void testMafftfromJava()

• testObjectAssignment

   static void testObjectAssignment()

• testChrMatch

   static void testChrMatch()

• getDataFromAssembly

   static void getDataFromAssembly(String assemblyFile, String outputFile)

• testChromLength

   static void testChromLength(String genome)

• getGenomeSequenceValues

   static void getGenomeSequenceValues()

• compareRefToReAssembledChrom

   static void compareRefToReAssembledChrom(String refGenome, String reAssembledChromFasta, String chrom, String coordinatesFile, String outputFile)

• createFindProteomeFile

   static void createFindProteomeFile()

• sortListCreatehash

   static void sortListCreatehash()

• testSortedRange

   static void testSortedRange()

• splitW22GenomeGetChrom10

   static void splitW22GenomeGetChrom10()

• countNsInFasta

   static void countNsInFasta()

• main

   static void main(Array<String> args)