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I understood the contig index incorrectly when I initially wrote this code. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-23 22:31:43 +00:00
parent 635bfd8604
commit 45d962e491
2 changed files with 23 additions and 12 deletions
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2
java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
View File

@ -167,7 +167,7 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
dataOfInterestStart = 0; dataOfInterestStart = 0;
} }
return new ReferenceSequence( contig, (int)start, accumulator ); return new ReferenceSequence( contig, sequenceDictionary.getSequenceIndex(contig), accumulator );
} }
/** /**

33
java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
View File

@ -56,7 +56,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,firstBasesOfChrM.length()-1); ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,firstBasesOfChrM.length()-1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertEquals( "First n bases of chrM are incorrect",
firstBasesOfChrM, firstBasesOfChrM,
StringUtil.bytesToString( sequence.getBases() ) ); StringUtil.bytesToString( sequence.getBases() ) );
@ -70,7 +71,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,extendedBasesOfChrM.length()-1); ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,extendedBasesOfChrM.length()-1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertEquals( "First n bases of chrM are incorrect",
extendedBasesOfChrM, extendedBasesOfChrM,
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );
@ -89,7 +91,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
bytesToChopOff + truncated.length() - 1); bytesToChopOff + truncated.length() - 1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertEquals( "First n bases of chrM are incorrect",
truncated, truncated,
StringUtil.bytesToString( sequence.getBases() ) ); StringUtil.bytesToString( sequence.getBases() ) );
@ -108,7 +111,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
bytesToChopOff + truncated.length() - 1); bytesToChopOff + truncated.length() - 1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertEquals( "First n bases of chrM are incorrect",
truncated, truncated,
StringUtil.bytesToString( sequence.getBases() ) ); StringUtil.bytesToString( sequence.getBases() ) );
@ -125,7 +129,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSequence("chrM"); ReferenceSequence sequence = sequenceFile.getSequence("chrM");
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals("chrM is incorrect", Assert.assertEquals("chrM is incorrect",
StringUtil.bytesToString(expectedSequence.getBases()), StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );
@ -167,7 +172,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSequence("chrY"); ReferenceSequence sequence = sequenceFile.getSequence("chrY");
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrY"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrY");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24);
Assert.assertEquals("chrY is incorrect", Assert.assertEquals("chrY is incorrect",
StringUtil.bytesToString(expectedSequence.getBases()), StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );
@ -185,7 +191,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSequence("chrX_random"); ReferenceSequence sequence = sequenceFile.getSequence("chrX_random");
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrX_random"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrX_random");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44);
Assert.assertEquals("chrX_random is incorrect", Assert.assertEquals("chrX_random is incorrect",
StringUtil.bytesToString(expectedSequence.getBases()), StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );
@ -200,7 +207,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",0,firstBasesOfChr1.length()-1); ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",0,firstBasesOfChr1.length()-1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr1"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
Assert.assertEquals( "First n bases of chr1 are incorrect", Assert.assertEquals( "First n bases of chr1 are incorrect",
firstBasesOfChr1, firstBasesOfChr1,
StringUtil.bytesToString( sequence.getBases() ) ); StringUtil.bytesToString( sequence.getBases() ) );
@ -214,7 +222,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",0,firstBasesOfChr8.length()-1); ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",0,firstBasesOfChr8.length()-1);
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr8"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr8");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8);
Assert.assertEquals( "First n bases of chr8 are incorrect", Assert.assertEquals( "First n bases of chr8 are incorrect",
firstBasesOfChr8, firstBasesOfChr8,
StringUtil.bytesToString( sequence.getBases() ) ); StringUtil.bytesToString( sequence.getBases() ) );
@ -231,7 +240,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.nextSequence(); ReferenceSequence sequence = sequenceFile.nextSequence();
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals("chrM is incorrect", Assert.assertEquals("chrM is incorrect",
StringUtil.bytesToString(expectedSequence.getBases()), StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );
@ -251,7 +261,8 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
ReferenceSequence sequence = sequenceFile.nextSequence(); ReferenceSequence sequence = sequenceFile.nextSequence();
long endTime = System.currentTimeMillis(); long endTime = System.currentTimeMillis();
Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr1"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
Assert.assertEquals("chr1 is incorrect", Assert.assertEquals("chr1 is incorrect",
StringUtil.bytesToString(expectedSequence.getBases()), StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) ); StringUtil.bytesToString(sequence.getBases()) );