<commit_before>package abra;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

/**
 * Simple ungapped alignment based upon initial exact seed match
 * @author lmose
 */
public class SimpleMapper {
	
	//TODO: May need to change for short reads or decreased maxMismatchRate
	//      Increasing when appropriate will speed things up.
	private static final int KMER_SIZE = 15;
	
	static final int UNMAPPED = -1;
	static final int HOMOLOGOUS_MAPPING = -2;
	
	static final char FORWARD_ORIENTATION = 0;
	static final char REVERSE_ORIENTATION = 1;
	
	enum Orientation {
		UNSET, FORWARD, REVERSE;
	}
	
	// Represents a single contig
	private String ref;
	private ReverseComplementor rc = new ReverseComplementor();
	private double maxMismatchRate;
	
	// kmer -> list of positions
	private Map<String, List<Integer>> kmerPositions = new HashMap<String, List<Integer>>();<commit_msg>Set SimpleMapper kmer_size to 10.<commit_after>package abra;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

/**
 * Simple ungapped alignment based upon initial exact seed match
 * @author lmose
 */
public class SimpleMapper {
	
	//TODO: May need to change for short reads or decreased maxMismatchRate
	//      Increasing when appropriate will speed things up.
	private static final int KMER_SIZE = 10;
	
	static final int UNMAPPED = -1;
	static final int HOMOLOGOUS_MAPPING = -2;
	
	static final char FORWARD_ORIENTATION = 0;
	static final char REVERSE_ORIENTATION = 1;
	
	enum Orientation {
		UNSET, FORWARD, REVERSE;
	}
	
	// Represents a single contig
	private String ref;
	private ReverseComplementor rc = new ReverseComplementor();
	private double maxMismatchRate;
	
	// kmer -> list of positions
	private Map<String, List<Integer>> kmerPositions = new HashMap<String, List<Integer>>();
{'fraction_non_alphanumeric': 0.08056133056133057, 'fraction_numerical': 0.007276507276507277, 'mean_word_length': 4.230978260869565, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 13, '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': '6328071', 'n_tokens_mistral': 631, 'n_tokens_neox': 574, 'n_words': 205}