fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1676 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
39a47491a9
commit
7bfb5fad27
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@ -52,7 +52,7 @@ 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("([\\w&&[^:]]+):([\\d,]+)?\\+?(-)?([\\d,]+)?$"); // matches case 3
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private static final Pattern mPattern = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)?(\\+)?(-)?([\\d,]+)?$"); // matches case 3
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// --------------------------------------------------------------------------------------------------------------
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@ -61,7 +61,7 @@ public class GenomeLocParser {
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//
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// --------------------------------------------------------------------------------------------------------------
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//public static Map<String, Integer> refContigOrdering = null;
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private static SAMSequenceDictionary contigInfo = null;
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protected static SAMSequenceDictionary contigInfo = null;
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/**
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* do we have a contig ordering setup?
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@ -140,12 +140,7 @@ 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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/*try {
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Thread.sleep(2000);
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} catch (InterruptedException e) {
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e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
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} */
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String contig = null;
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long start = 1;
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long stop = Integer.MAX_VALUE;
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@ -156,32 +151,24 @@ public class GenomeLocParser {
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try {
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if (match.matches()) {
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contig = match.group(1);
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if (match.groupCount() > 1) {
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switch (match.groupCount()) {
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case 2:
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start = stop = parsePosition(match.group(2));
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break;
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case 3:
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start = parsePosition(match.group(2));
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if (!match.group(3).equals("+")) bad = true;
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break;
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case 4:
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start = parsePosition(match.group(2));
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stop = parsePosition(match.group(4));
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break;
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default:
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if (match.groupCount() == 5) {
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start = parsePosition(match.group(2));
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if (match.group(3) != null && match.group(3).equals("+") && match.group(5) == null) {
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// do nothing
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} else if (match.group(5) != null)
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stop = parsePosition(match.group(5));
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else if (match.group(5) == null && match.group(4) == null && match.group(3) == null)
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stop = start;
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else
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bad = true;
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break;
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} else {
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bad = true;
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}
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}
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} else {
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bad = true;
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}
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}
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catch (Exception e) {
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bad = true;
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bad = true;
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}
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if (bad)
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@ -194,6 +181,7 @@ public class GenomeLocParser {
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if (!isContigValid(contig))
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throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
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GenomeLoc loc = parseGenomeLoc(contig, start, stop);
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return loc;
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}
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@ -75,7 +75,7 @@ public class rodDbSNPTest extends BaseTest {
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stop = (var.getLocation().getContig().equals("1") && var.getLocation().getStart() > 11000000);
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line = stream.readLine();
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}
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Assert.assertEquals(3717,snpCount);
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Assert.assertEquals(3615,snpCount);
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Assert.assertEquals(9902,indelCount);
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} catch (IOException e) {
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@ -3,16 +3,11 @@ package org.broadinstitute.sting.utils;
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import static junit.framework.Assert.assertTrue;
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import net.sf.samtools.SAMFileHeader;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import static org.junit.Assert.assertEquals;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.LinkedList;
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import java.util.List;
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/**
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* @author aaron
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@ -22,15 +17,22 @@ import java.util.List;
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* Test out the functionality of the new genome loc parser
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*/
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public class GenomeLocParserTest extends BaseTest {
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@Test(expected = StingException.class)
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public void testUnsetupException() {
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GenomeLocParser.contigInfo = null;
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GenomeLocParser.createGenomeLoc(0, 0, 0);
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}
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@BeforeClass
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public static void init() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
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GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
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}
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@Test
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public void testKnownContigOrder() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
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GenomeLocParser.contigInfo = null;
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// assert that it's false when the contig ordering is not setup
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assertTrue(!GenomeLocParser.hasKnownContigOrdering());
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GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
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@ -97,6 +99,14 @@ public class GenomeLocParserTest extends BaseTest {
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assertEquals(1, loc.getStart());
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}
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@Test
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public void testCreateGenomeLoc1point5() { // in honor of VAAL!
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GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1");
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assertEquals(loc.getContigIndex(), 0);
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assertEquals(1, loc.getStop());
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assertEquals(1, loc.getStart());
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}
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@Test
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public void testCreateGenomeLoc2() {
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GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1, 100);
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@ -130,7 +140,7 @@ public class GenomeLocParserTest extends BaseTest {
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assertEquals(1, copy.getStart());
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}
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@Test
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/*@Test // - uncomment if you want to test speed
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public void testGenomeLocParserList() {
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long start = System.currentTimeMillis();
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List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(Arrays.asList(new String[]{"/humgen/gsa-scr1/GATK_Data/Validation_Data/bigChr1IntervalList.list"}));
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@ -138,5 +148,21 @@ public class GenomeLocParserTest extends BaseTest {
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LinkedList<GenomeLoc> loc = new LinkedList<GenomeLoc>(GenomeLocParser.mergeOverlappingLocations(parsedIntervals));
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long stop = System.currentTimeMillis();
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logger.warn("Elapsed time = " + (stop - start));
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}*/
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@Test
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public void testGenomeLocPlusSign() {
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GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1+");
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assertEquals(0, loc.getContigIndex());
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assertEquals(10, loc.getStop()); // the size
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assertEquals(1, loc.getStart());
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}
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@Test(expected = RuntimeException.class)
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public void testGenomeLocBad() {
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GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-");
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assertEquals(0, loc.getContigIndex());
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assertEquals(10, loc.getStop()); // the size
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assertEquals(1, loc.getStart());
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}
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}
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