net.maizegenetics.dna.map

Interface GVCFGenomeSequence

All Superinterfaces:

GenomeSequence

public GVCFGenomeSequence
extends GenomeSequence

Created by zrm22 on 3/27/17. Interface is used to store GenomeSequences defined by a GATK generated GVCF file

Method Detail

getChrPosMap

java.util.Map<net.maizegenetics.dna.map.Chromosome,kotlin.Array[]> getChrPosMap()

getGVCFPositions

PositionList getGVCFPositions()

getConsecutiveRegions

java.util.HashMap<net.maizegenetics.dna.map.Chromosome,java.util.ArrayList> getConsecutiveRegions()

getMaskBitSet

BitSet getMaskBitSet()

setMaskBitSet

void setMaskBitSet(BitSet newMaskBitSet)

getFilterBitSet

BitSet getFilterBitSet()

setFilterBitSet

void setFilterBitSet(BitSet newFilterBitSet)

flipMaskBit

void flipMaskBit(int index)

flipFilterBit

void flipFilterBit(int index)

writeFASTA

void writeFASTA(java.lang.String fileName)

chromosomeSequenceAndStats

java.util.HashMap<java.lang.String,java.lang.String> chromosomeSequenceAndStats(Chromosome chrom,
                                                                                int startSite,
                                                                                int lastSite)

getPreviousRegionStats

java.util.HashMap<java.lang.String,java.lang.Integer> getPreviousRegionStats()

resetCounters

void resetCounters()