net.maizegenetics.pangenome.hapcollapse

Class PurgeSequencesFromAlignments

java.lang.Object

net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments

public class PurgeSequencesFromAlignments
extends Object

Created by edbuckler on 6/19/17.

Field Summary

Fields

Modifier and Type	Field and Description
static String	anchorSummaryFile
static String	localDirectory
static String	localDirectoryOut
static String	loggingFile

Constructor Summary

Constructors

Constructor and Description
PurgeSequencesFromAlignments()

Method Summary

Modifier and Type	Method and Description
static Optional<net.maizegenetics.dna.snp.GenotypeTable>	filterBadAlignments(net.maizegenetics.dna.snp.GenotypeTable genotypeTable, double maxDist, int minSiteCount, double minMAF) This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

localDirectory

public static final String localDirectory

See Also:

Constant Field Values

localDirectoryOut

public static final String localDirectoryOut

See Also:

Constant Field Values

loggingFile

public static final String loggingFile

See Also:

Constant Field Values

anchorSummaryFile

public static final String anchorSummaryFile

See Also:

Constant Field Values

Constructor Detail

PurgeSequencesFromAlignments

public PurgeSequencesFromAlignments()

Method Detail

main

public static void main(String[] args)

filterBadAlignments

public static Optional<net.maizegenetics.dna.snp.GenotypeTable> filterBadAlignments(net.maizegenetics.dna.snp.GenotypeTable genotypeTable,
                                                                                    double maxDist,
                                                                                    int minSiteCount,
                                                                                    double minMAF)

This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF

Parameters:

genotypeTable -

maxDist -

minSiteCount -

minMAF -

Returns: