net.maizegenetics.pangenome.hapcollapse

Class QualityReportAnchorsToHaplotypes

java.lang.Object

net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes

public class QualityReportAnchorsToHaplotypes
extends Object

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

Field Summary

Fields

Modifier and Type	Field and Description
static String	alignmentFiltered
static String	alignmentRaw
static String	anchorIDFile
static String	consensusHaplotypes
static String	reportFile
static String	workdir

Constructor Summary

Constructors

Constructor and Description
QualityReportAnchorsToHaplotypes()

Method Summary

Modifier and Type	Method and Description
static String	comparaRawFilteredAlignment(String inMSA, String outMSA)
static double	distanceAllTaxaToGivenTaxa(net.maizegenetics.taxa.distance.DistanceMatrix matrixDistance, String taxaName)
static double	distanceTaxaPair(net.maizegenetics.taxa.distance.DistanceMatrix matrixDistance, String taxaPairOne, String taxaPairTwo)
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

workdir

public static final String workdir

See Also:

Constant Field Values

anchorIDFile

public static final String anchorIDFile

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Constant Field Values

alignmentRaw

public static final String alignmentRaw

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Constant Field Values

alignmentFiltered

public static final String alignmentFiltered

See Also:

Constant Field Values

consensusHaplotypes

public static final String consensusHaplotypes

See Also:

Constant Field Values

reportFile

public static final String reportFile

See Also:

Constant Field Values

Constructor Detail

QualityReportAnchorsToHaplotypes

public QualityReportAnchorsToHaplotypes()

Method Detail

comparaRawFilteredAlignment

public static String comparaRawFilteredAlignment(String inMSA,
                                                 String outMSA)
                                          throws IOException

Throws:

IOException

main

public static void main(String[] args)

distanceAllTaxaToGivenTaxa

public static double distanceAllTaxaToGivenTaxa(net.maizegenetics.taxa.distance.DistanceMatrix matrixDistance,
                                                String taxaName)

distanceTaxaPair

public static double distanceTaxaPair(net.maizegenetics.taxa.distance.DistanceMatrix matrixDistance,
                                      String taxaPairOne,
                                      String taxaPairTwo)