net.maizegenetics.dna.map

Class TagMappingInfoV3

net.maizegenetics.dna.map.TagMappingInfoV3

public class TagMappingInfoV3

Container class for information on mapping position.

The mappingSource can be an identifier. Byte.MIN_VALUE means the tag doesn't exist (missing) in the mapping result. Other values means it exist in mapping result. The result could be either mapped or unmapped. Note: BWA doesn't provide mapping score, so the rank is just based on the order provided for multiple hits Note: Currently, perfectMatch of PE is unknown (Byte.MIN_VALUE);

Field Detail

chromosome

public int chromosome

Chromosome as an integer, unknown = Integer.MIN_VALUE

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, unknown = Integer.MIN_VALUE

endPosition

public int endPosition

Chromosomal position of the common adapter end of the tag (smaller than startPosition if tag matches minus strand), inclusive, unknown = Integer.MIN_VALUE

divergence

public byte divergence

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

perfectMatch

public byte perfectMatch

If the alignment is a perfect match to the reference, y = 1, n = 0, unknown = Byte.MIN_VALUE

mappingSource

public byte mappingSource

Code of mappingSource.0: Bowtie2; 1: BWA; 2: BLAST; 3: BWAMEM; 4: PE one end; 5: PE the other end; 6: Genetic Mapping; missing = Byte.MIN_VALUE

mappingRank

public byte mappingRank

The rank of this mapping based on the scores from one aligner, starting from 0. If there are two 0, the rank of the third one is 1

mappingScore

public short mappingScore

The mapping score of this mapping, 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

TagMappingInfoV3

public TagMappingInfoV3()

TagMappingInfoV3

public TagMappingInfoV3(int chromosome,
                        byte strand,
                        int startPosition,
                        int endPosition,
                        byte divergence,
                        byte perfectMatch,
                        byte mappingSource,
                        short mappingScore)

TagMappingInfoV3

public TagMappingInfoV3(int chromosome,
                        byte strand,
                        int startPosition,
                        int endPosition,
                        byte divergence,
                        byte perfectMatch,
                        byte mappingSource,
                        short mappingScore,
                        kotlin.Array[] variantPosOff,
                        kotlin.Array[] variantDef,
                        byte dcoP,
                        byte mapP)

Method Detail

setMappingRank

public void setMappingRank(byte mappingRank)

setMappingSource

public void setMappingSource(byte mappingSource)