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- All Implemented Interfaces:
public class QualityReportAnchorsToHaplotypes
Created 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 String
workdir
public final static String
anchorIDFile
public final static String
alignmentRaw
public final static String
alignmentFiltered
public final static String
consensusHaplotypes
public final static String
reportFile
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Method Summary
Modifier and Type Method Description static String
comparaRawFilteredAlignment(String inMSA, String outMSA)
static void
main(Array<String> args)
static double
distanceAllTaxaToGivenTaxa(DistanceMatrix matrixDistance, String taxaName)
static double
distanceTaxaPair(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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