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Inserted a dangerous (but hidden) command-line argument for use by the Picard team. 

Used to process intervals over BAMs without indices.  Tim understands the risks but
wants this anyway, as a temporary solution to a pipeline problem.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5148 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-01-31 22:10:06 +00:00
parent 6c99dc4dab
commit 391f248640
2 changed files with 9 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -387,7 +387,7 @@ public class GenomeAnalysisEngine {
if(readsDataSource != null && !readsDataSource.hasIndex() ) { if(readsDataSource != null && !readsDataSource.hasIndex() ) {
if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM)) if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported."); throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.");
if(intervals != null) if(intervals != null && !argCollection.allowIntervalsWithUnindexedBAM)
throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available."); throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");
Shard.ShardType shardType; Shard.ShardType shardType;

8
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -237,6 +237,11 @@ public class GATKArgumentCollection {
@Hidden @Hidden
public int processTrackerID = -1; public int processTrackerID = -1;
@Element(required = false)
@Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM. NO INTEGRATION TESTS are available. Use at your own risk.")
@Hidden
public boolean allowIntervalsWithUnindexedBAM = false;
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //
// methods // methods
@ -420,6 +425,9 @@ public class GATKArgumentCollection {
if ( processTrackerID != other.processTrackerID ) if ( processTrackerID != other.processTrackerID )
return false; return false;
if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
return false;
return true; return true;
} }