net.maizegenetics.dna.map

Class TagMappingInfo

net.maizegenetics.dna.map.TagMappingInfo

public class TagMappingInfo

Container class for information on mapping position.

TODO: Needs to be generalized for describing all mapping positions.

Field Detail

chromosome

public int chromosome

Chromosome as an integer

strand

public byte strand

Strand relative to reference genome. 1 = same sense as reference FASTA file. -1 = opposite sense. unknown = Byte.MIN_VALUE

startPosition

public int startPosition

Chromosomal position of the barcoded end of the tag

endPosition

public int endPosition

Chromosomal position of the common adapter end of the tag (smaller than startPosition if tag matches minus strand)

divergence

public byte divergence

Number of diverging bp (edit distance) from reference, unknown = Byte.MIN_VALUE

dcoP

public byte dcoP

Double cross-over probability Round(Log2(P)), unknown Byte.MIN_VALUE

mapP

public byte mapP

Genetic mapping probability Round(Log2(P)), unknown Byte.MIN_VALUE

Constructor Detail

TagMappingInfo

public TagMappingInfo()

TagMappingInfo

public TagMappingInfo(int chromosome,
                      byte strand,
                      int startPosition,
                      int endPosition,
                      byte divergence)

TagMappingInfo

public TagMappingInfo(int chromosome,
                      byte strand,
                      int startPosition,
                      int endPosition,
                      byte divergence,
                      kotlin.Array[] variantPosOff,
                      kotlin.Array[] variantDef,
                      byte dcoP,
                      byte mapP)