public class KmerToTBTPlugin
extends AbstractPlugin
This pipeline converts a series of fastq files to TagsByTaxa files (one per fastq file). It requires a list of existing tags (Tags object), which may come from a TagCounts file or TOPM file.
public KmerToTBTPlugin()
public KmerToTBTPlugin(java.awt.Frame parentFrame)
public void setParameters(java.lang.String[] args)
public static void matchTagsToTaxa(java.lang.String[] fastqFileS,
Tags theMasterTags,
java.lang.String outputDir,
int minCount,
boolean useTBTByte,
boolean useTBTShort)
Uses an existing Tags object to create one TagsByTaxa file for each fastq file in the input directory. Output TBT files written to the outputDir, using fastq file names with extension changed to .tbt.bin (or .tbt.txt)
fastqFileS - Array of fastq file names (Illumina-created files with raw read sequence, quality score, machine name, etc.)theMasterTags - A Tags object: list of tags to be included in the final TBToutputDir - String containing the path of the output directory to contain tags-by-taxa filesminCount - The minimum number of times a tag must show up in a fastq file before it is included in the corresponding TBT filepublic javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()