net.maizegenetics.dna.snp.io

Class ReadBedfile

net.maizegenetics.dna.snp.io.ReadBedfile

public class ReadBedfile

Method Detail

getRanges

public static java.util.List<net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange> getRanges(java.lang.String bedFile)

Function to parse the bedFile and create a List of BedFileRanges. The positions stored in BedFileRange are 1-based inclusive exclusive. This is done by adding 1 to both the start and end position from the BED file.

Parameters:

bedFile -

Returns:

org.jetbrains.dokka.NodeRenderContent@53397ce9:

getPositionList

public static PositionList getPositionList(java.lang.String bedfile)

Gets position list from specified bed file.

Returns:

org.jetbrains.dokka.NodeRenderContent@562c567e: position list

getRangesAsPositions

public static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> getRangesAsPositions(java.lang.String bedfile)

Function that returns the 1-based Position ranges from a BED file as a RangeSet of Positions. NOTE: getRanges(bedFile) will be called which will shift the start and end positions in the BED file up by 1. Because of this the ranges returned will be 1-based Closed-Open(Inclusive-Exclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).

Parameters:

bedfile -

Returns:

org.jetbrains.dokka.NodeRenderContent@a093cb8:

getClosedRangesAsPositions

public static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> getClosedRangesAsPositions(java.lang.String bedfile)

Function that returns the 1-based closed Position ranges from a BED file as a RangeSet of Positions. NOTE: getRanges(bedFile) will be called which will shift the start in the BED file up by 1. Because of this the ranges returned will be 1-based Closed(Inclusive-Inclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).

Parameters:

bedfile -

Returns:

org.jetbrains.dokka.NodeRenderContent@4e6b9cae:

getRangesAsPositionMap

public static com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,java.lang.String> getRangesAsPositionMap(java.lang.String bedfile)

Function that returns the 1-based Position ranges from a BED file as a RangeMap of Positions to the annotated name of the region. NOTE: getRanges(bedFile) will be called which will shift the start and end positions in the BED file up by 1. Because of this the ranges returned will be 1-based Closed-Open(Inclusive-Exclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).

Parameters:

bedfile -

Returns:

org.jetbrains.dokka.NodeRenderContent@56ad7fbe: