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small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2011-01-05 21:20:26 +00:00
parent 20f29e4690
commit cba436fa2f
2 changed files with 10 additions and 5 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
View File

@ -13,7 +13,7 @@ import java.io.IOException;
import java.util.*; import java.util.*;
/** /**
* implementation of a simple table (tab or comma delimited format) input files... more improvements to come * implementation of a simple table (tab or comma delimited format) input files
*/ */
public class TableCodec implements ReferenceDependentFeatureCodec { public class TableCodec implements ReferenceDependentFeatureCodec {
private String delimiterRegex = "\\s+"; private String delimiterRegex = "\\s+";
@ -48,8 +48,6 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
String[] split = line.split(delimiterRegex); String[] split = line.split(delimiterRegex);
if (split.length < 1) if (split.length < 1)
throw new IllegalArgumentException("TableCodec line = " + line + " doesn't appear to be a valid table format"); throw new IllegalArgumentException("TableCodec line = " + line + " doesn't appear to be a valid table format");
return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split),header); return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split),header);
} }
@ -67,6 +65,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line); if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line);
String spl[] = line.split(delimiterRegex); String spl[] = line.split(delimiterRegex);
for (String s : spl) header.add(s); for (String s : spl) header.add(s);
return header;
} else if (!line.startsWith(commentDelimiter)) { } else if (!line.startsWith(commentDelimiter)) {
break; break;
} }

10
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java
View File

@ -51,6 +51,10 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
private GenomeLoc testSite2; private GenomeLoc testSite2;
private GenomeLoc testSite3; private GenomeLoc testSite3;
private GenomeLoc testInterval1; // an interval matching testSite1 -> testSite2 for queries
private GenomeLoc testInterval2; // an interval matching testSite2 -> testSite3 for queries
@BeforeClass @BeforeClass
public void init() throws FileNotFoundException { public void init() throws FileNotFoundException {
seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference)); seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
@ -59,6 +63,8 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
testSite1 = genomeLocParser.createGenomeLoc("chrM",10); testSite1 = genomeLocParser.createGenomeLoc("chrM",10);
testSite2 = genomeLocParser.createGenomeLoc("chrM",20); testSite2 = genomeLocParser.createGenomeLoc("chrM",20);
testSite3 = genomeLocParser.createGenomeLoc("chrM",30); testSite3 = genomeLocParser.createGenomeLoc("chrM",30);
testInterval1 = genomeLocParser.createGenomeLoc("chrM",10,20);
testInterval2 = genomeLocParser.createGenomeLoc("chrM",20,30);
} }
@BeforeMethod @BeforeMethod
@ -92,10 +98,10 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
@Test @Test
public void testCreateMultipleIterators() { public void testCreateMultipleIterators() {
ReferenceOrderedQueryDataPool iteratorPool = new ReferenceOrderedQueryDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser); ReferenceOrderedQueryDataPool iteratorPool = new ReferenceOrderedQueryDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser);
LocationAwareSeekableRODIterator iterator1 = iteratorPool.iterator( new EntireStream() ); LocationAwareSeekableRODIterator iterator1 = iteratorPool.iterator( new MappedStreamSegment(testInterval1) );
// Create a new iterator at position 2. // Create a new iterator at position 2.
LocationAwareSeekableRODIterator iterator2 = iteratorPool.iterator( new EntireStream() ); LocationAwareSeekableRODIterator iterator2 = iteratorPool.iterator( new MappedStreamSegment(testInterval2) );
Assert.assertEquals(iteratorPool.numIterators(), 2, "Number of iterators in the pool is incorrect"); Assert.assertEquals(iteratorPool.numIterators(), 2, "Number of iterators in the pool is incorrect");
Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect"); Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");