From ca2cd9d4f5cf383a33758232cfd6676eea5d3263 Mon Sep 17 00:00:00 2001 From: aaron Date: Wed, 3 Mar 2010 16:31:45 +0000 Subject: [PATCH] a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/utils/sam/ArtificialSAMUtils.java | 10 ++++++---- .../providers/ReadBasedReferenceOrderedViewTest.java | 7 +------ .../sting/gatk/refdata/ReadMetaDataTrackerTest.java | 6 +----- 3 files changed, 8 insertions(+), 15 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index 5618bcdf4..5004292f1 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -154,11 +154,13 @@ public class ArtificialSAMUtils { elements.add(new CigarElement(length, CigarOperator.characterToEnum('M'))); record.setCigar(new Cigar(elements)); record.setProperPairFlag(false); - // TODO: add to code after checking why it breaks the clean read injector test - /*byte[] c = new byte[length]; + + // our reads are all 'A's by default + byte[] c = new byte[length]; for (int x = 0; x < length; x++) - c[x] = 'A'; */ - //record.setReadBases(c); + c[x] = 'A'; + record.setReadBases(c); + if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { record.setReadUmappedFlag(true); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewTest.java index a74beb7ff..ce3eb045e 100644 --- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewTest.java @@ -73,12 +73,7 @@ public class ReadBasedReferenceOrderedViewTest extends BaseTest { // make ten reads, List records = new ArrayList(); for (int x = 1; x < 11; x++) { - SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, "name", 0, x, 10); - byte[] c = new byte[10]; - for (int y = 0; y < 10; y++) - c[y] = 'A'; - rec.setReadBases(c); - records.add(rec); + SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, "name", 0, x, 10); } GenomeLoc start = GenomeLocParser.createGenomeLoc(0,0,0); List list = new ArrayList(); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerTest.java index e84d66a9a..3ef325905 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerTest.java @@ -107,11 +107,7 @@ public class ReadMetaDataTrackerTest extends BaseTest { } private ReadMetaDataTracker getRMDT(int incr) { - SAMRecord record = ArtificialSAMUtils.createArtificialRead(header, "name", 0, 1, 10); - byte[] c = new byte[10]; - for (int x = 0; x < 10; x++) - c[x] = 'A'; - record.setReadBases(c); + SAMRecord record = ArtificialSAMUtils.createArtificialRead(header, "name", 0, 1, 10); TreeMap> data = new TreeMap>(); for (int x = 0; x < record.getAlignmentEnd(); x+=incr) { GenomeLoc loc = GenomeLocParser.createGenomeLoc(record.getReferenceIndex(), record.getAlignmentStart() + x, record.getAlignmentStart() + x);