net.maizegenetics.dna.tag

Class TagCountMutable

AbstractTags

TagCounts

net.maizegenetics.dna.tag.TagCountMutable

All Implemented Interfaces:

Tags

Direct Known Subclasses:

UTagCountMutable

public class TagCountMutable
extends TagCounts

Resizeable tags count container. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified.

Constructor Detail

TagCountMutable

public TagCountMutable(int tagLengthInLong,
                       int maxSize)

TagCountMutable

public TagCountMutable(Tags origTagCount,
                       int maxSize)

Method Detail

initMatrices

protected void initMatrices(int tagNum)

getCurrentSize

public int getCurrentSize()

addReadCount

public void addReadCount(kotlin.Array[] tag,
                         int length,
                         int count)

addReadCounts

public void addReadCounts(TagCounts tagCountsToAdd)

This adds a series of TagCounts to the list, preserving the count that each read has. Designed to make it easy to combine TagCounts from multiple barcodes, lanes or flowcells.

Parameters:

tagCountsToAdd -

addReadCounts

public void addReadCounts(Tags tagsToAdd,
                          int defaultCount)

collapseCounts

public void collapseCounts()

removeRareTag

public void removeRareTag(int minCutoff)

shrinkToCurrentRows

public int shrinkToCurrentRows()

compare

public int compare(int index1,
                   int index2)