Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3522 348d0f76-0448-11de-a6fe-93d51630548a
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weisburd
parent
20167fd411
commit
adc4c4e577
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@ -25,25 +25,24 @@
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package org.broadinstitute.sting.utils;
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import net.sf.picard.util.IntervalList;
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import net.sf.picard.util.Interval;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
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import org.broadinstitute.sting.utils.bed.BedParser;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.picard.util.Interval;
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import net.sf.picard.util.IntervalList;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
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import org.broadinstitute.sting.utils.bed.BedParser;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.text.XReadLines;
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/**
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* Created by IntelliJ IDEA.
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@ -55,7 +54,7 @@ import java.util.regex.Pattern;
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public class GenomeLocParser {
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private static Logger logger = Logger.getLogger(GenomeLocParser.class);
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private static final Pattern mPattern = Pattern.compile("([\\p{Print}&&[^:]]+):*([\\d,]+)?([\\+-])?([\\d,]+)?$"); // matches case 3
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//private static final Pattern mPattern = Pattern.compile("([\\p{Print}&&[^:]]+):*([\\d,]+)?([\\+-])?([\\d,]+)?$"); // matches case 3
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// --------------------------------------------------------------------------------------------------------------
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@ -137,7 +136,7 @@ public class GenomeLocParser {
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/**
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* parse a genome interval, from a location string
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*
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* Performs interval-style validation:
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* Performs interval-style validation:
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*
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* contig is valid; start and stop less than the end; start <= sto
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* @param str the string to parse
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@ -154,8 +153,8 @@ public class GenomeLocParser {
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/**
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* parse a genome location, from a location string
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*
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* Performs read-style validation:
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*
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* Performs read-style validation:
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* checks that start and stop are positive, start < stop, and the contig is valid
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* does not check that genomeLoc is actually on the contig
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*
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@ -167,40 +166,41 @@ public class GenomeLocParser {
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public static GenomeLoc parseGenomeLoc(final String str) {
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// 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
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//System.out.printf("Parsing location '%s'%n", str);
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String contig = null;
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long start = 1;
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long stop = -1;
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boolean bad = false;
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Matcher match = mPattern.matcher(str);
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try {
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if (match.matches() && match.groupCount() == 4) {
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if (match.group(1) != null) contig = match.group(1);
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if (match.group(2) != null) start = parsePosition(match.group(2));
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if ((match.group(3) != null && match.group(3).equals("+")) || // chr:1+
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(match.group(3) == null && match.group(4) == null && match.group(2) == null)) // chr1
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stop = Integer.MAX_VALUE;
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else if (match.group(3) != null && match.group(3).equals("-")) // chr1:1-1
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stop = parsePosition(match.group(4));
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else if (match.group(3) == null && match.group(4) == null) // chr1:1
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stop = start;
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else {
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bad = true;
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final int colonIndex = str.indexOf(":");
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if(colonIndex == -1) {
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contig = str.substring(0, str.length()); // chr1
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stop = Integer.MAX_VALUE;
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} else {
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contig = str.substring(0, colonIndex);
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final int dashIndex = str.indexOf('-', colonIndex);
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try {
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if(dashIndex == -1) {
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if(str.charAt(str.length() - 1) == '+') {
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start = parsePosition(str.substring(colonIndex + 1, str.length() - 1)); // chr:1+
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stop = Integer.MAX_VALUE;
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} else {
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start = parsePosition(str.substring(colonIndex + 1)); // chr1:1
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stop = start;
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}
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} else {
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start = parsePosition(str.substring(colonIndex + 1, dashIndex)); // chr1:1-1
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stop = parsePosition(str.substring(dashIndex + 1));
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}
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} catch(Exception e) {
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throw new StingException("Failed to parse Genome Location string: " + str, e);
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}
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} catch (Exception e) {
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bad = true;
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}
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if (bad)
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throw new StingException("Failed to parse Genome Location string: " + str);
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// is the contig valid?
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if (!isContigValid(contig))
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throw new StingException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?");
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throw new StingException("Contig '" + contig + "' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?");
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if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
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if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
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// lookup the actually stop position!
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stop = getContigInfo(contig).getSequenceLength();
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@ -214,9 +214,24 @@ public class GenomeLocParser {
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// Parsing string representations
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//
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// --------------------------------------------------------------------------------------------------------------
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/**
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* Parses a number like 1,000,000 into a long.
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* @param pos
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*/
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private static long parsePosition(final String pos) {
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String x = pos.replaceAll(",", "");
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return Long.parseLong(x);
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//String x = pos.replaceAll(",", ""); - this was replaced because it uses regexps
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if(pos.indexOf(',') != -1) {
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final StringBuilder buffer = new StringBuilder();
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for(int i = 0; i < pos.length(); i++) {
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final char c = pos.charAt(i);
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if(c != ',') {
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buffer.append(c);
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}
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}
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return Long.parseLong(buffer.toString());
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} else {
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return Long.parseLong(pos);
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}
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}
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@ -457,11 +472,11 @@ public class GenomeLocParser {
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/**
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* verify the specified genome loc is valid, if it's not, throw an exception
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* Will not verify the location against contig bounds.
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*
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*
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* Validation:
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* checks that start and stop are positive, start < stop, and the contig is valid
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* does not check that genomeLoc is actually on the contig, so start could be > end of contig
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*
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* Validation:
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* checks that start and stop are positive, start < stop, and the contig is valid
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* does not check that genomeLoc is actually on the contig, so start could be > end of contig
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*
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* @param toReturn the genome loc we're about to return
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*
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