zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add removeProgramRecords argument 

* Add unit test for the removeProgramRecords
This commit is contained in:
Joel Thibault 2012-07-30 10:19:57 -04:00
parent d53105668b
commit 2b25df3d53
4 changed files with 95 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -813,7 +813,8 @@ public class GenomeAnalysisEngine {
getWalkerBAQQualityMode(),
refReader,
getBaseRecalibration(),
argCollection.defaultBaseQualities);
argCollection.defaultBaseQualities,
argCollection.removeProgramRecords);
}
/**

3
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -249,6 +249,9 @@ public class GATKArgumentCollection {
@Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
@Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we remove program records from the SAM header", required = false)
public boolean removeProgramRecords = false;
@Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime. For expert users only who know what they are doing. We do not support usage of this argument.", required = false)
public ValidationExclusion.TYPE unsafe;

21
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -89,6 +89,11 @@ public class SAMDataSource {
*/
private final SAMFileReader.ValidationStringency validationStringency;
/**
* Do we want to remove the program records from this data source?
*/
private final boolean removeProgramRecords;
/**
* Store BAM indices for each reader present.
*/
@ -200,7 +205,8 @@ public class SAMDataSource {
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1);
(byte) -1,
false);
}
/**
@ -233,7 +239,8 @@ public class SAMDataSource {
BAQ.QualityMode qmode,
IndexedFastaSequenceFile refReader,
BaseRecalibration bqsrApplier,
byte defaultBaseQualities) {
byte defaultBaseQualities,
boolean removeProgramRecords) {
this.readMetrics = new ReadMetrics();
this.genomeLocParser = genomeLocParser;
@ -249,6 +256,7 @@ public class SAMDataSource {
dispatcher = null;
validationStringency = strictness;
this.removeProgramRecords = removeProgramRecords;
if(readBufferSize != null)
ReadShard.setReadBufferSize(readBufferSize);
else {
@ -748,7 +756,7 @@ public class SAMDataSource {
private synchronized void createNewResource() {
if(allResources.size() > maxEntries)
throw new ReviewedStingException("Cannot create a new resource pool. All resources are in use.");
SAMReaders readers = new SAMReaders(readerIDs, validationStringency);
SAMReaders readers = new SAMReaders(readerIDs, validationStringency, removeProgramRecords);
allResources.add(readers);
availableResources.add(readers);
}
@ -777,9 +785,11 @@ public class SAMDataSource {
/**
* Derive a new set of readers from the Reads metadata.
* @param readerIDs reads to load.
* TODO: validationStringency is not used here
* @param validationStringency validation stringency.
* @param removeProgramRecords indicate whether to clear program records from the readers
*/
public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) {
public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency, boolean removeProgramRecords) {
final int totalNumberOfFiles = readerIDs.size();
int readerNumber = 1;
final SimpleTimer timer = new SimpleTimer().start();
@ -790,6 +800,9 @@ public class SAMDataSource {
long lastTick = timer.currentTime();
for(final SAMReaderID readerID: readerIDs) {
final ReaderInitializer init = new ReaderInitializer(readerID).call();
if (removeProgramRecords) {
init.reader.getFileHeader().setProgramRecords(new ArrayList<SAMProgramRecord>());
}
if (threadAllocation.getNumIOThreads() > 0) {
inputStreams.put(init.readerID, init.blockInputStream); // get from initializer
}

73
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java
View File

@ -24,9 +24,12 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMProgramRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.Tags;
@ -36,6 +39,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.AfterMethod;
@ -143,4 +147,73 @@ public class SAMDataSourceUnitTest extends BaseTest {
fail("testLinearBreakIterateAll: We Should get a UserException.CouldNotReadInputFile exception");
}
}
/** Test that we clear program records when requested */
@Test
public void testRemoveProgramRecords() {
logger.warn("Executing testRemoveProgramRecords");
// setup the data
readers.add(new SAMReaderID(new File(b37GoodBAM),new Tags()));
// use defaults
SAMDataSource data = new SAMDataSource(readers,
new ThreadAllocation(),
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
false);
List<SAMProgramRecord> defaultProgramRecords = data.getHeader().getProgramRecords();
assertTrue(defaultProgramRecords.size() != 0, "testRemoveProgramRecords: No program records found when using default constructor");
boolean removeProgramRecords = false;
data = new SAMDataSource(readers,
new ThreadAllocation(),
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1,
removeProgramRecords);
List<SAMProgramRecord> dontRemoveProgramRecords = data.getHeader().getProgramRecords();
assertEquals(dontRemoveProgramRecords, defaultProgramRecords, "testRemoveProgramRecords: default program records differ from removeProgramRecords = false");
removeProgramRecords = true;
data = new SAMDataSource(readers,
new ThreadAllocation(),
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1,
removeProgramRecords);
List<SAMProgramRecord> doRemoveProgramRecords = data.getHeader().getProgramRecords();
assertTrue(doRemoveProgramRecords.isEmpty(), "testRemoveProgramRecords: program records not cleared when removeProgramRecords = true");
}
}