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oops - we don't need reference bases, but we still need reference 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1653 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-18 16:24:45 +00:00
parent 2b2df4e1ba
commit 90626c843d
4 changed files with 4 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java
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@ -27,7 +27,7 @@ import java.util.*;
* Copies reads from the input stream into the <code>outputBAM</code>, replacing those * Copies reads from the input stream into the <code>outputBAM</code>, replacing those
* reads which have been cleaned with their new clean copies. * reads which have been cleaned with their new clean copies.
*/ */
@Requires({DataSource.READS}) @Requires({DataSource.READS, DataSource.REFERENCE})
public class CleanedReadInjector extends ReadWalker<Integer,Integer> { public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
/** /**

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java
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@ -16,7 +16,7 @@ import java.util.List;
// although this can easily be changed if necessary. // although this can easily be changed if necessary.
@WalkerName("IndelIntervals") @WalkerName("IndelIntervals")
@Requires({DataSource.READS}) @Requires({DataSource.READS, DataSource.REFERENCE})
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> { public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> {
@Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false) @Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
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@ -39,7 +39,7 @@ import java.util.*;
* Merges intervals based on reads which overlap them. * Merges intervals based on reads which overlap them.
*/ */
@WalkerName("IntervalMerger") @WalkerName("IntervalMerger")
@Requires({DataSource.READS}) @Requires({DataSource.READS, DataSource.REFERENCE})
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
public class IntervalMergerWalker extends ReadWalker<Integer,Integer> { public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@WalkerName("SNPClusters") @WalkerName("SNPClusters")
@Requires(value={},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)}) @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)})
public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> { public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false) @Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false)
int windowSize = 10; int windowSize = 10;