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Merge branch 'unstable' of github.com:broadinstitute/cmi-gatk into unstable

This commit is contained in:
Guillermo del Angel 2012-10-12 14:49:37 -04:00
parent 32e377a0db 274ac4836f
commit 7e1657d243
4 changed files with 35 additions and 32 deletions
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17
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -181,15 +181,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
private double minIndelProportionToTriggerVariant = 0.05;
/**
* Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
* considered consensus.
*/
@Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
private int nContigs = 2;
/**
* Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
* A value of 0 turns downsampling off.
@ -197,6 +188,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
private int downsampleCoverage = 250;
/**
* Number of chromossomes in the sample (this is used for the polyploid consensus compression). Only
* tested for humans (or organisms with n=2). Use at your own risk!
*/
@Hidden
@Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
private int nContigs = 2;
@Hidden
@Argument(fullName = "", shortName = "dl", doc = "", required = false)
private int debugLevel = 0;

36
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -124,32 +124,28 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
// This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
// therefore, the user must have failed to specify a type default
if(writerFileName == null) {
if(!source.isRequired())
throw new MissingArgumentValueException(bamArgumentDefinition);
if(generateMD5)
if(writerFileName == null && generateMD5)
throw new ArgumentException("MD5 generation specified, but no output file specified. If md5 generation is desired, please specify a BAM output file and an md5 file will be written alongside.");
}
// Create the stub and set parameters.
SAMFileWriterStub stub;
if ( writerFileName != null )
SAMFileWriterStub stub = null; // stub = new SAMFileWriterStub(engine, defaultOutputStream);
if ( writerFileName != null ) {
stub = new SAMFileWriterStub(engine, new File(writerFileName));
else
stub = new SAMFileWriterStub(engine, defaultOutputStream);
if ( compressionLevel != null )
stub.setCompressionLevel(compressionLevel);
if ( indexOnTheFly )
stub.setIndexOnTheFly(indexOnTheFly);
if ( generateMD5 )
stub.setGenerateMD5(generateMD5);
if ( simplifyBAM )
stub.setSimplifyBAM(simplifyBAM);
if ( compressionLevel != null )
stub.setCompressionLevel(compressionLevel);
if ( indexOnTheFly )
stub.setIndexOnTheFly(indexOnTheFly);
if ( generateMD5 )
stub.setGenerateMD5(generateMD5);
if ( simplifyBAM )
stub.setSimplifyBAM(simplifyBAM);
// WARNING: Side effects required by engine!
parsingEngine.addTags(stub,getArgumentTags(matches));
engine.addOutput(stub);
// WARNING: Side effects required by engine!
parsingEngine.addTags(stub,getArgumentTags(matches));
engine.addOutput(stub);
}
return stub;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -370,8 +370,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
currentInterval = intervals.hasNext() ? intervals.next() : null;
writerToUse = writer;
if ( N_WAY_OUT != null ) {
boolean createIndex = true;
@ -383,9 +381,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
createIndex, generateMD5s,createProgramRecord(),KEEP_ALL_PG_RECORDS);
}
} else {
// set up the output writer
setupWriter(getToolkit().getSAMFileHeader());
writerToUse = writer;
}
manager = new ConstrainedMateFixingManager(writerToUse, getToolkit().getGenomeLocParser(), MAX_ISIZE_FOR_MOVEMENT, MAX_POS_MOVE_ALLOWED, MAX_RECORDS_IN_MEMORY);

10
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -113,4 +113,14 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
executeTest(String.format("realigner [%s]", entry.getKey()), spec);
}
}
@Test
public void testNWayOut() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommandPrefix + " -nWayOut .clean.bam ",
1,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e"));
executeTest("test realigner nWayOut", spec1);
}
}