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public class QualityReportAnchorsToHaplotypesCreated by mm2842 on 6/20/17. Check the output of AnchorFastaReader.java using GenotypeTools for stats check some of the input files vs the expected output (check that it is working as expected) files in the box files are Ed code's output The output files will be tested and a logging file with stats will be output
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Field Summary
Fields Modifier and Type Field Description public final static Stringworkdirpublic final static StringanchorIDFilepublic final static StringalignmentRawpublic final static StringalignmentFilteredpublic final static StringconsensusHaplotypespublic final static StringreportFile
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Method Summary
Modifier and Type Method Description static StringcomparaRawFilteredAlignment(String inMSA, String outMSA)static voidmain(Array<String> args)static doubledistanceAllTaxaToGivenTaxa(DistanceMatrix matrixDistance, String taxaName)static doubledistanceTaxaPair(DistanceMatrix matrixDistance, String taxaPairOne, String taxaPairTwo)-
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Method Detail
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comparaRawFilteredAlignment
static String comparaRawFilteredAlignment(String inMSA, String outMSA)
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distanceAllTaxaToGivenTaxa
static double distanceAllTaxaToGivenTaxa(DistanceMatrix matrixDistance, String taxaName)
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distanceTaxaPair
static double distanceTaxaPair(DistanceMatrix matrixDistance, String taxaPairOne, String taxaPairTwo)
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