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Merge pull request #289 from broadinstitute/md_fix_bq 

Bugfix: defaultBaseQualities actually works now
This commit is contained in:
MauricioCarneiro 2013-06-18 11:58:39 -07:00
parent 1c400e8f8e 7b22467148
commit 6a5502c94a
4 changed files with 42 additions and 11 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -187,6 +187,12 @@ public class GATKArgumentCollection {
@Argument(fullName = "allow_potentially_misencoded_quality_scores", shortName="allowPotentiallyMisencodedQuals", doc="Do not fail when encountering base qualities that are too high and that seemingly indicate a problem with the base quality encoding of the BAM file", required = false)
public boolean ALLOW_POTENTIALLY_MISENCODED_QUALS = false;
@Argument(fullName="useOriginalQualities", shortName = "OQ", doc = "If set, use the original base quality scores from the OQ tag when present instead of the standard scores", required=false)
public Boolean useOriginalBaseQualities = false;
@Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
public byte defaultBaseQualities = -1;
// --------------------------------------------------------------------------------------------------------------
//
// performance log arguments
@ -201,9 +207,6 @@ public class GATKArgumentCollection {
@Argument(fullName = "performanceLog", shortName="PF", doc="If provided, a GATK runtime performance log will be written to this file", required = false)
public File performanceLog = null;
@Argument(fullName="useOriginalQualities", shortName = "OQ", doc = "If set, use the original base quality scores from the OQ tag when present instead of the standard scores", required=false)
public Boolean useOriginalBaseQualities = false;
// --------------------------------------------------------------------------------------------------------------
//
// BQSR arguments
@ -267,9 +270,6 @@ public class GATKArgumentCollection {
//
// --------------------------------------------------------------------------------------------------------------
@Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
public byte defaultBaseQualities = -1;
@Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -630,6 +630,10 @@ public class SAMDataSource {
// * (otherwise we will process something that we may end up throwing away) * //
// ************************************************************************************************ //
if (useOriginalBaseQualities || defaultBaseQualities >= 0)
// only wrap if we are replacing the original qualities or using a default base quality
wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities);
// Filters:
wrappedIterator = StingSAMIteratorAdapter.adapt(new CountingFilteringIterator(readMetrics,wrappedIterator,supplementalFilters));
@ -654,10 +658,6 @@ public class SAMDataSource {
if (!noValidationOfReadOrder && enableVerification)
wrappedIterator = new VerifyingSamIterator(wrappedIterator);
if (useOriginalBaseQualities || defaultBaseQualities >= 0)
// only wrap if we are replacing the original qualities or using a default base quality
wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities);
// set up read transformers
for ( final ReadTransformer readTransformer : readTransformers ) {
if ( readTransformer.enabled() && readTransformer.getApplicationTime() == ReadTransformer.ApplicationTime.ON_INPUT )

5
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
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@ -234,7 +234,10 @@ public class MalformedReadFilter extends ReadFilter {
else if (filterMismatchingBaseAndQuals)
result = false;
else
throw new UserException.MalformedBAM(read, String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals]", read.getReadName(), read.getReadLength(), read.getBaseQualities().length));
throw new UserException.MalformedBAM(read,
String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals].%s",
read.getReadName(), read.getReadLength(), read.getBaseQualities().length,
read.getBaseQualities().length == 0 ? " You can use --defaultBaseQualities to assign a default base quality for all reads, but this can be dangerous in you don't know what you are doing." : ""));
return result;
}

28
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
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@ -227,4 +227,32 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
nLines++;
Assert.assertTrue(nLines > 0);
}
// --------------------------------------------------------------------------------
//
// Test that defaultBaseQualities actually works
//
// --------------------------------------------------------------------------------
public WalkerTestSpec testDefaultBaseQualities(final Integer value, final String md5) {
return new WalkerTestSpec("-T PrintReads -R " + b37KGReference + " -I " + privateTestDir + "/baseQualitiesToFix.bam -o %s"
+ (value != null ? " --defaultBaseQualities " + value : ""),
1, Arrays.asList(md5));
}
@Test()
public void testDefaultBaseQualities20() {
executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "7d254a9d0ec59c66ee3e137f56f4c78f"));
}
@Test()
public void testDefaultBaseQualities30() {
executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "0f50def6cbbbd8ccd4739e2b3998e503"));
}
@Test(expectedExceptions = Exception.class)
public void testDefaultBaseQualitiesNoneProvided() {
executeTest("testDefaultBaseQualitiesNoneProvided", testDefaultBaseQualities(null, ""));
}
}