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

Part III of GSA-462: Consistent RODBinding access across Ref and Read trackers 

-- shardSpan is only calculated when there some ROD is live in the GATK.  No sense in paying the cost per read when you don't need it
-- Update contract to allow null span or unmapped span (good catch unittests!)
This commit is contained in:
Mark DePristo 2012-08-29 17:44:35 -04:00
parent 1200848bbf
commit 53376b9423
1 changed files with 7 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
View File

@ -57,7 +57,9 @@ public class ReadBasedReferenceOrderedView implements View {
private final GenomeLoc shardSpan; private final GenomeLoc shardSpan;
public ReadBasedReferenceOrderedView(final ShardDataProvider provider) { public ReadBasedReferenceOrderedView(final ShardDataProvider provider) {
this(provider.getGenomeLocParser(), ((ReadShard)provider.getShard()).getReadsSpan()); this.genomeLocParser = provider.getGenomeLocParser();
// conditional to optimize the case where we don't have any ROD data
this.shardSpan = provider.getReferenceOrderedData() != null ? ((ReadShard)provider.getShard()).getReadsSpan() : null;
provider.register(this); provider.register(this);
if ( provider.getReferenceOrderedData() != null && ! shardSpan.isUnmapped() ) { if ( provider.getReferenceOrderedData() != null && ! shardSpan.isUnmapped() ) {
@ -66,10 +68,6 @@ public class ReadBasedReferenceOrderedView implements View {
} }
} }
private ReadBasedReferenceOrderedView(final GenomeLocParser genomeLocParser, final GenomeLoc shardSpan) {
this.genomeLocParser = genomeLocParser;
this.shardSpan = shardSpan;
}
/** /**
* Testing constructor * Testing constructor
@ -78,7 +76,8 @@ public class ReadBasedReferenceOrderedView implements View {
final GenomeLoc shardSpan, final GenomeLoc shardSpan,
final List<String> names, final List<String> names,
final List<PeekableIterator<RODRecordList>> featureSources) { final List<PeekableIterator<RODRecordList>> featureSources) {
this(genomeLocParser, shardSpan); this.genomeLocParser = genomeLocParser;
this.shardSpan = shardSpan;
for ( int i = 0; i < names.size(); i++ ) for ( int i = 0; i < names.size(); i++ )
states.add(new RMDDataState(names.get(i), featureSources.get(i))); states.add(new RMDDataState(names.get(i), featureSources.get(i)));
} }
@ -106,10 +105,10 @@ public class ReadBasedReferenceOrderedView implements View {
return getReferenceOrderedDataForInterval(genomeLocParser.createGenomeLoc(rec)); return getReferenceOrderedDataForInterval(genomeLocParser.createGenomeLoc(rec));
} }
@Requires({"interval != null", "shardSpan.containsP(interval)"}) @Requires({"interval != null", "shardSpan == null || shardSpan.isUnmapped() || shardSpan.containsP(interval)"})
@Ensures("result != null") @Ensures("result != null")
public RefMetaDataTracker getReferenceOrderedDataForInterval(final GenomeLoc interval) { public RefMetaDataTracker getReferenceOrderedDataForInterval(final GenomeLoc interval) {
if ( states.isEmpty() ) // optimization for no bindings (common for read walkers) if ( states.isEmpty() || shardSpan.isUnmapped() ) // optimization for no bindings (common for read walkers)
return EMPTY_TRACKER; return EMPTY_TRACKER;
else { else {
final List<RODRecordList> bindings = new ArrayList<RODRecordList>(states.size()); final List<RODRecordList> bindings = new ArrayList<RODRecordList>(states.size());