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

Minor updates to match the wiki documentation. 

Upper cased the PartitionType enum values.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5506 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-03-24 20:22:23 +00:00
parent 1281c842ad
commit e47513f043
6 changed files with 9 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
View File

@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorFilter; import org.broadinstitute.sting.gatk.iterators.LocusIteratorFilter;
import net.sf.picard.filter.SamRecordFilter;
import java.util.List; import java.util.List;
import java.util.Arrays; import java.util.Arrays;
@ -19,7 +18,7 @@ import java.util.Arrays;
*/ */
@By(DataSource.READS) @By(DataSource.READS)
@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES}) @Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
@PartitionBy(PartitionType.Interval) @PartitionBy(PartitionType.INTERVAL)
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckReadFilter.class}) @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckReadFilter.class})
public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> { public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
// Do we actually want to operate on the context? // Do we actually want to operate on the context?

8
java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java
View File

@ -32,23 +32,23 @@ public enum PartitionType {
/** /**
* Do not partition the walker inputs. * Do not partition the walker inputs.
*/ */
None, NONE,
/** /**
* The walker inputs can be chunked down to the * The walker inputs can be chunked down to the
* per-locus level. * per-locus level.
*/ */
Locus, LOCUS,
/** /**
* The walker inputs should be processed as complete * The walker inputs should be processed as complete
* intervals defined -L or the reference contigs. * intervals defined -L or the reference contigs.
*/ */
Interval, INTERVAL,
/** /**
* The walker inputs should always be processed as complete * The walker inputs should always be processed as complete
* contigs, even if there are multiple intervals per contig. * contigs, even if there are multiple intervals per contig.
*/ */
Contig CONTIG
} }

2
java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
View File

@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
@Requires({DataSource.READS, DataSource.REFERENCE_BASES}) @Requires({DataSource.READS, DataSource.REFERENCE_BASES})
@PartitionBy(PartitionType.Contig) @PartitionBy(PartitionType.CONTIG)
public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> { public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
public boolean requiresOrderedReads() { return false; } public boolean requiresOrderedReads() { return false; }

2
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
View File

@ -42,7 +42,7 @@ import org.apache.log4j.Logger;
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
@ReadFilters(MalformedReadFilter.class) @ReadFilters(MalformedReadFilter.class)
@PartitionBy(PartitionType.None) @PartitionBy(PartitionType.NONE)
@BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT) @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
public abstract class Walker<MapType, ReduceType> { public abstract class Walker<MapType, ReduceType> {
final protected static Logger logger = Logger.getLogger(Walker.class); final protected static Logger logger = Logger.getLogger(Walker.class);

5
java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -41,7 +41,6 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescripto
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -213,9 +212,9 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
*/ */
private String getScatterClass(Class<? extends Walker> walkerType) { private String getScatterClass(Class<? extends Walker> walkerType) {
PartitionType partitionType = walkerType.getAnnotation(PartitionBy.class).value(); PartitionType partitionType = walkerType.getAnnotation(PartitionBy.class).value();
if (partitionType == PartitionType.None) if (partitionType == PartitionType.NONE)
return null; return null;
return partitionType.name() + "ScatterFunction"; return StringUtils.capitalize(partitionType.name().toLowerCase()) + "ScatterFunction";
} }
/** /**

1
scala/qscript/examples/ExampleUnifiedGenotyper.scala
View File

@ -4,7 +4,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._
/** /**
* An example building on the intro ExampleCountReads.scala. * An example building on the intro ExampleCountReads.scala.
* Runs an INCOMPLETE version of the UnifiedGenotyper with VariantEval and optional VariantFiltration. * Runs an INCOMPLETE version of the UnifiedGenotyper with VariantEval and optional VariantFiltration.
* If run on a compute cluster, splits the UnifiedGenotyper into 3 parts.
*/ */
class ExampleUnifiedGenotyper extends QScript { class ExampleUnifiedGenotyper extends QScript {
// Create an alias 'qscript' to be able to access variables // Create an alias 'qscript' to be able to access variables