net.maizegenetics.dna.tag

Class AbstractPETags

net.maizegenetics.dna.tag.AbstractPETags

All Implemented Interfaces:

PETags

Direct Known Subclasses:

AbstractPETagsOnPhysicalMap, PETagCounts

public class AbstractPETags
implements PETags

Basic methods for working with PE Tags, including sorting and search.

Field Detail

tagLengthInLong

protected int tagLengthInLong

Tag length in Long primitive data type

tagsF

protected kotlin.Array[] tagsF

Forward tags in Long array Columns are sequence, rows are index of sequence. This is faster than the other way

tagsB

protected kotlin.Array[] tagsB

Backward tags in Long array Columns are sequence, rows are index of sequence. This is faster than the other way

tagFLength

protected kotlin.Array[] tagFLength

Length of forward tags

tagBLength

protected kotlin.Array[] tagBLength

Length of backward tags

contigLengthInLong

protected kotlin.Array[] contigLengthInLong

Length of contigs in Long primitive data type, 0 means contig doesn't exist

contig

protected kotlin.Array[] contig

Contigs in Long array

contigLength

protected kotlin.Array[] contigLength

Length of contigs, 0 means contig doesn't exist

Method Detail

getTagF

public kotlin.Array[] getTagF(int index)

getTagB

public kotlin.Array[] getTagB(int index)

getTagCount

public int getTagCount()

getTagIndex

public int getTagIndex(kotlin.Array[] tagF,
                       kotlin.Array[] tagB)

getContig

public kotlin.Array[] getContig(int index)

getContigCount

public int getContigCount()

getContigLength

public short getContigLength(int index)

getContigLengthInLong

public byte getContigLengthInLong(int index)

mkFastaFile

public void mkFastaFile(java.lang.String fFastaFileS,
                        java.lang.String bFastaFileS)

Write forword and backword fasta files of PE tag for Bowtie2 alignment, the sequence is in format of index_f/b_c/n, where f means forward, b means backword, c means contig, n means no contig When contig exist, the forward and backword tags are the contig and reverse complement of the contig, respectively.

Parameters:

fFastaFileS -

bFastaFileS -

mkFastaFile

public void mkFastaFile(java.lang.String tagsFFastaFileS,
                        java.lang.String tagsBFastaFileS,
                        java.lang.String contigFastaFileS)

Deprecated.

Write fasta files of PE tag for alignment

Parameters:

tagsFFastaFileS -

tagsBFastaFileS -

contigFastaFileS -

orderTagsFTagsB

public void orderTagsFTagsB()

Order forward and backward tags

contigPETags

public void contigPETags()

Make contigs from forward and backward tags

getTagFLength

public short getTagFLength(int index)

getTagBLength

public short getTagBLength(int index)

getTagSizeInLong

public int getTagSizeInLong()

iniMatrix

protected void iniMatrix(int tagLengthInLong,
                         int tagNum)

Initialize the matrix of data structure extending AbstractPETags

Parameters:

tagLengthInLong -

tagNum -

swap

public void swap(int index1,
                 int index2)

Swap two PE tags

Parameters:

index1 -

index2 -

compare

public int compare(int index1,
                   int index2)

Compare two PE tags

Parameters:

index1 - index of the first PE tag

index2 - index of the second PE tag

Returns:

org.jetbrains.dokka.NodeRenderContent@5b55c169: result of comparison from two PE tags -1(<), 0(=), 1(>)

sort

public void sort()

sort PE tags by Long primitive data type value