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

Optimizations in VCFCodec 

-- Don't create an empty LinkedHashSet() for PASS fields.   Just return Collections.emptySet() instead.
-- For filter fields with actual values, returns an unmodifiableSet instead of one that can be changed
This commit is contained in:
Mark DePristo 2011-09-02 08:46:17 -04:00
parent c3ea96d856
commit c57198a1b9
1 changed files with 4 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -110,11 +110,8 @@ public class VCFCodec extends AbstractVCFCodec {
if ( filterString.equals(VCFConstants.UNFILTERED) ) if ( filterString.equals(VCFConstants.UNFILTERED) )
return null; return null;
// empty set for passes filters
LinkedHashSet<String> fFields = new LinkedHashSet<String>();
if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) )
return fFields; return Collections.emptySet();
if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) ) if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) )
generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4"); generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4");
if ( filterString.length() == 0 ) if ( filterString.length() == 0 )
@ -124,6 +121,8 @@ public class VCFCodec extends AbstractVCFCodec {
if ( filterHash.containsKey(filterString) ) if ( filterHash.containsKey(filterString) )
return filterHash.get(filterString); return filterHash.get(filterString);
// empty set for passes filters
LinkedHashSet<String> fFields = new LinkedHashSet<String>();
// otherwise we have to parse and cache the value // otherwise we have to parse and cache the value
if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 ) if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 )
fFields.add(filterString); fFields.add(filterString);
@ -132,7 +131,7 @@ public class VCFCodec extends AbstractVCFCodec {
filterHash.put(filterString, fFields); filterHash.put(filterString, fFields);
return fFields; return Collections.unmodifiableSet(fFields);
} }