net.maizegenetics.analysis.gbs.repgen

Class AlignmentInfo

net.maizegenetics.analysis.gbs.repgen.AlignmentInfo

public class AlignmentInfo

This class is used by RepGenAlignerPlugin to store alignment info to db table tagAlignments. It is also used when pulling alignments from the DB. The tag2chrom and tag2pos fields are used to determine if the tag2 of this alignment class is a reference tag. If tag2chrom is null and tag2pos = -1, the tag alignment info is a non-ref tag. If these fields are populated with good values, the tag2 alignment info is for a reference tag. The "alignmentPos" field indicates the position within tag2 where the tag1 alignment starts. This position is adjusted for any clipping of tag1 that occurred during alignment.

Constructor Detail

AlignmentInfo

public AlignmentInfo(Tag tag2,
                     java.lang.String chromosome,
                     int position,
                     int alignmentpos,
                     int ref_strand,
                     java.lang.String ref_genome,
                     int score)

Method Detail

tag2

public Tag tag2()

tag2chrom

public java.lang.String tag2chrom()

tag2pos

public int tag2pos()

alignmentPos

public int alignmentPos()

ref_strand

public int ref_strand()

ref_genome

public java.lang.String ref_genome()

score

public int score()

toString

public java.lang.String toString()

compareTo

public int compareTo(AlignmentInfo other)