<commit_before>package org.seqcode.projects.sequnwinder.framework;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Random;
import java.util.Set;

import org.seqcode.data.io.RegionFileUtilities;
import org.seqcode.data.motifdb.WeightMatrix;
import org.seqcode.genome.Genome;
import org.seqcode.genome.GenomeConfig;
import org.seqcode.genome.location.NamedRegion;
import org.seqcode.genome.location.Point;
import org.seqcode.genome.location.Region;
import org.seqcode.genome.location.RepeatMaskedRegion;
import org.seqcode.genome.sequence.SequenceGenerator;
import org.seqcode.gsebricks.verbs.location.ChromRegionIterator;
import org.seqcode.gsebricks.verbs.location.RepeatMaskedGenerator;
import org.seqcode.gseutils.ArgParser;
import org.seqcode.gseutils.Args;


/**
 * @author akshaykakumanu
 * @twitter ikaka89
 * @email <EMAIL>
 */
public class SeqUnwinderConfig implements Serializable{
	
	/**
	 * 
	 */
	private static final long serialVersionUID = 1L;

	public static String version = "0.1.2";
	
	// General options
	protected GenomeConfig gcon;
	protected SequenceGenerator<Region> seqgen = null;
	protected RepeatMaskedGenerator<Region> repMask;
	protected String[] args;<commit_msg>Defining version 0.1.3, which fixes issue with calculation of AUROCs for final MEME-processed motifs. <commit_after>package org.seqcode.projects.sequnwinder.framework;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Random;
import java.util.Set;

import org.seqcode.data.io.RegionFileUtilities;
import org.seqcode.data.motifdb.WeightMatrix;
import org.seqcode.genome.Genome;
import org.seqcode.genome.GenomeConfig;
import org.seqcode.genome.location.NamedRegion;
import org.seqcode.genome.location.Point;
import org.seqcode.genome.location.Region;
import org.seqcode.genome.location.RepeatMaskedRegion;
import org.seqcode.genome.sequence.SequenceGenerator;
import org.seqcode.gsebricks.verbs.location.ChromRegionIterator;
import org.seqcode.gsebricks.verbs.location.RepeatMaskedGenerator;
import org.seqcode.gseutils.ArgParser;
import org.seqcode.gseutils.Args;


/**
 * @author akshaykakumanu
 * @twitter ikaka89
 * @email <EMAIL>
 */
public class SeqUnwinderConfig implements Serializable{
	
	/**
	 * 
	 */
	private static final long serialVersionUID = 1L;

	public static String version = "0.1.3";
	
	// General options
	protected GenomeConfig gcon;
	protected SequenceGenerator<Region> seqgen = null;
	protected RepeatMaskedGenerator<Region> repMask;
	protected String[] args;
{'fraction_non_alphanumeric': 0.10205412455167917, 'fraction_numerical': 0.00489077274209325, 'mean_word_length': 5.684095860566448, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6744776', 'n_tokens_mistral': 1007, 'n_tokens_neox': 959, 'n_words': 199}