net.maizegenetics.dna.tag

Class TagCounts

AbstractTags

net.maizegenetics.dna.tag.TagCounts

All Implemented Interfaces:

Tags

Direct Known Subclasses:

TagCountMutable

public class TagCounts
extends AbstractTags

Holds tags counts. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified. This class is not resizable in terms of new tags - for growing tag count lists use TagCountMutable.java User: ed

Constructor Detail

TagCounts

public TagCounts()

TagCounts

public TagCounts(int tagLengthInLong,
                 int maxSize)

TagCounts

public TagCounts(java.lang.String inFile,
                 net.maizegenetics.dna.tag.TagsByTaxa.FilePacking binary)

Method Detail

readDistFile

public void readDistFile(java.lang.String infile,
                         net.maizegenetics.dna.tag.TagsByTaxa.FilePacking binary)

initMatrices

protected void initMatrices(int tagNum)

toFASTA

public void toFASTA(java.lang.String outfile)

Convert TagCounts to FASTA file for alignment using Blast

Parameters:

outfile -

toFASTQ

public void toFASTQ(java.lang.String infile,
                    java.lang.String outfile)

Reads in a binary tag count file line-by-line and constructs a FASTQ file for alignment.

readBinaryTagCountFile

public void readBinaryTagCountFile(java.io.File inFile)

writeTagCountFile

public void writeTagCountFile(java.lang.String outFile,
                              net.maizegenetics.dna.tag.TagsByTaxa.FilePacking binary,
                              int minCount)

getReadCount

public int getReadCount(int index)

Parameters:

index - Array index of the read whose count this function should return.

tagsWCountsGreaterThanMin

protected kotlin.Array[] tagsWCountsGreaterThanMin(int minCount)

setTag

public void setTag(kotlin.Array[] sequence,
                   byte length,
                   int count,
                   int index)

sort

public void sort()

printRows

protected void printRows(int numRows)

collapseCounts

protected void collapseCounts()

getSize

public int getSize()

getTotalCount

public int getTotalCount()

swap

public void swap(int index1,
                 int index2)

compare

public int compare(int index1,
                   int index2)

compare

public byte compare(kotlin.Array[] sequence1,
                    kotlin.Array[] sequence2)

getTagIndexSet

public kotlin.Array[] getTagIndexSet(kotlin.Array[] read)

areTagsUnique

public boolean areTagsUnique()

getTagSizeInLong

public int getTagSizeInLong()

getTagLength

public int getTagLength(int index)

getTagCount

public int getTagCount()

I don't know why we have 4 or 5 methods with different names that do exactly the same thing. I'm just putting this here because it's defined in the abstract class and its absence is causing problems.

Returns:

org.jetbrains.dokka.NodeRenderContent@b782b70: The number of tags in the current object's tags[][] matrix.

getTags

public kotlin.Array[] getTags()