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changes to make GenomeLoc string parsing 25% faster 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1675 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-21 22:37:47 +00:00
parent b1dc6d65e4
commit 39a47491a9
2 changed files with 52 additions and 35 deletions
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67
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -52,10 +52,7 @@ import java.util.regex.Pattern;
public class GenomeLocParser {
private static Logger logger = Logger.getLogger(GenomeLocParser.class);
private static final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1
private static final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2
private static final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3
private static final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4
private static final Pattern mPattern = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)?\\+?(-)?([\\d,]+)?$"); // matches case 3
// --------------------------------------------------------------------------------------------------------------
@ -143,57 +140,61 @@ public class GenomeLocParser {
public static GenomeLoc parseGenomeLoc(final String str) {
// 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
//System.out.printf("Parsing location '%s'%n", str);
/*try {
Thread.sleep(2000);
} catch (InterruptedException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
} */
String contig = null;
long start = 1;
long stop = Integer.MAX_VALUE;
boolean bad = false;
Matcher match1 = regex1.matcher(str);
Matcher match2 = regex2.matcher(str);
Matcher match3 = regex3.matcher(str);
Matcher match4 = regex4.matcher(str);
Matcher match = mPattern.matcher(str);
try {
if (match1.matches()) {
contig = match1.group(1);
} else if (match2.matches()) {
contig = match2.group(1);
start = parsePosition(match2.group(2));
stop = start;
} else if (match4.matches()) {
contig = match4.group(1);
start = parsePosition(match4.group(2));
} else if (match3.matches()) {
contig = match3.group(1);
start = parsePosition(match3.group(2));
stop = parsePosition(match3.group(3));
if (match.matches()) {
contig = match.group(1);
if (match.groupCount() > 1) {
switch (match.groupCount()) {
case 2:
start = stop = parsePosition(match.group(2));
break;
case 3:
start = parsePosition(match.group(2));
if (!match.group(3).equals("+")) bad = true;
break;
case 4:
start = parsePosition(match.group(2));
stop = parsePosition(match.group(4));
break;
default:
bad = true;
break;
if (start > stop)
bad = true;
}
}
} else {
bad = true;
}
} catch (Exception e) {
bad = true;
}
if (bad) {
throw new StingException("Invalid Genome Location string: " + str);
catch (Exception e) {
bad = true;
}
if (stop == Integer.MAX_VALUE && hasKnownContigOrdering()) {
if (bad)
throw new StingException("Invalid Genome Location string: "); // + str);
if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
// lookup the actually stop position!
stop = getContigInfo(contig).getSequenceLength();
}
if (!isContigValid(contig))
throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
GenomeLoc loc = parseGenomeLoc(contig, start, stop);
// System.out.printf(" => Parsed location '%s' into %s%n", str, loc);
return loc;
}

20
java/test/org/broadinstitute/sting/utils/GenomeLocParserTest.java
View File

@ -3,10 +3,16 @@ package org.broadinstitute.sting.utils;
import static junit.framework.Assert.assertTrue;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import static org.junit.Assert.assertEquals;
import org.junit.Test;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
/**
* @author aaron
@ -117,10 +123,20 @@ public class GenomeLocParserTest extends BaseTest {
@Test
public void testCreateGenomeLoc5() {
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0,1,100);
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1, 100);
GenomeLoc copy = GenomeLocParser.createGenomeLoc(loc);
assertEquals(copy.getContigIndex(), 0);
assertEquals(100, copy.getStop());
assertEquals(1, copy .getStart());
assertEquals(1, copy.getStart());
}
@Test
public void testGenomeLocParserList() {
long start = System.currentTimeMillis();
List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(Arrays.asList(new String[]{"/humgen/gsa-scr1/GATK_Data/Validation_Data/bigChr1IntervalList.list"}));
Collections.sort(parsedIntervals);
LinkedList<GenomeLoc> loc = new LinkedList<GenomeLoc>(GenomeLocParser.mergeOverlappingLocations(parsedIntervals));
long stop = System.currentTimeMillis();
logger.warn("Elapsed time = " + (stop - start));
}
}