diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index 15da66f2e82ce030489516c0494f21eeec784682..6ed6d75a7d6578107f8f9cd425b0fba829eba821 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -59,7 +59,7 @@ public class VCFFilter extends JFrame
{
private static final long serialVersionUID = 1L;
- private static boolean useHeader = true;
+ //private static boolean useHeader = true;
/* private static int MIN_DP = 0;
private static float MIN_MQ = 0;
private static float MIN_AF1 = 0;
@@ -263,7 +263,7 @@ public class VCFFilter extends JFrame
if(info.size() == 0)
{
- useHeader = false;
+ //useHeader = false;
/* // min DP
c.gridy = c.gridy+1;
c.gridx = 0;
@@ -368,7 +368,7 @@ public class VCFFilter extends JFrame
String hdrLine = "##FILTER=<ID="+id+",Type=Flag,Number=0,Description=\""+descr+"\">";
HeaderLine hLine = new HeaderLine(hdrLine, HeaderLine.filterFlagStr[hdrIndex],
AbstractVCFReader.getLineHash("FILTER", hdrLine));
- FilteredPanel.addFilter(ID, hLine, 0);
+ filterPanel.addFilter(ID, hLine, 0);
}
else
filterPanel.removeFilter(ID);
@@ -431,7 +431,7 @@ public class VCFFilter extends JFrame
{
final String ID = hLine.getHeaderTypeStr()+":"+hLine.getID();
if(flag.isSelected())
- FilteredPanel.addFilter(ID, hLine, 0);
+ filterPanel.addFilter(ID, hLine, 0);
else
filterPanel.removeFilter(ID);
filterPanel.updateFilters();
@@ -572,110 +572,105 @@ public class VCFFilter extends JFrame
}
}
- if(useHeader)
+ final Hashtable<String, RecordFilter> filters = FilteredPanel.getFilters();
+ final Enumeration<String> enumFilter = filters.keys();
+ while(enumFilter.hasMoreElements())
{
- Hashtable<String, RecordFilter> filters = FilteredPanel.getFilters();
-
- Enumeration<String> enumFilter = filters.keys();
- while(enumFilter.hasMoreElements())
- {
- String recid = enumFilter.nextElement();
- RecordFilter recFilter = filters.get(recid);
- String id = recFilter.getHeaderLine().getID();
+ final String recid = enumFilter.nextElement();
+ final RecordFilter recFilter = filters.get(recid);
+ final String id = recFilter.getHeaderLine().getID();
- switch (recFilter.getHeaderLine().getHeaderType())
- {
- case HeaderLine.FILTER_NV_FLAG: // FILTER non-variant
- if( record.getAlt().isNonVariant() )
- return false;
- break;
- case HeaderLine.FILTER_INS:
- if( record.getAlt().isInsertion(vcfReader.isVcf_v4()) )
- return false;
- break;
- case HeaderLine.FILTER_DEL:
- if( record.getAlt().isDeletion(vcfReader.isVcf_v4()) )
- return false;
- break;
- case HeaderLine.FILTER_OVERLAP_FLAG: // FILTER no overlap
- if( !VCFview.isOverlappingFeature(features, basePosition) )
+ switch (recFilter.getHeaderLine().getHeaderType())
+ {
+ case HeaderLine.FILTER_NV_FLAG: // FILTER non-variant
+ if( record.getAlt().isNonVariant() )
+ return false;
+ break;
+ case HeaderLine.FILTER_INS:
+ if( record.getAlt().isInsertion(vcfReader.isVcf_v4()) )
+ return false;
+ break;
+ case HeaderLine.FILTER_DEL:
+ if( record.getAlt().isDeletion(vcfReader.isVcf_v4()) )
+ return false;
+ break;
+ case HeaderLine.FILTER_OVERLAP_FLAG: // FILTER no overlap
+ if( !VCFview.isOverlappingFeature(features, basePosition) )
+ return false;
+ break;
+ case HeaderLine.INFO_LINE: // INFO line
+ if (recFilter.getHeaderLine().isFlag())
+ {
+ if(record.containsInfoFlag(id))
return false;
- break;
- case HeaderLine.INFO_LINE: // INFO line
- if (recFilter.getHeaderLine().isFlag())
- {
- if(record.containsInfoFlag(id))
- return false;
- continue;
- }
- else
- {
- String inf = record.getInfoValue(id);
- if(inf == null || !recFilter.pass(record, inf.split(","), vcfReader))
- return false;
- }
- break;
- case HeaderLine.FORMAT_LINE: // FORMAT Genotype line
- final String samples[] = record.getFormatValues(id);
- if(samples == null)
+ continue;
+ }
+ else
+ {
+ String inf = record.getInfoValue(id);
+ if(inf == null || !recFilter.pass(record, inf.split(","), vcfReader))
return false;
-
- if (recFilter.getHeaderLine().isFlag())
- return true;
+ }
+ break;
+ case HeaderLine.FORMAT_LINE: // FORMAT Genotype line
+ final String samples[] = record.getFormatValues(id);
+ if(samples == null)
+ return false;
+ if (recFilter.getHeaderLine().isFlag())
+ return true;
- if(sampleIndex > -1) // look at a specific sample
+ if(sampleIndex > -1) // look at a specific sample
+ {
+ if(samples[sampleIndex] == null || !recFilter.pass(record, samples[sampleIndex].split(","), vcfReader))
+ return false;
+ }
+ else // look at all samples
+ {
+ for(int i=0; i<samples.length; i++)
{
- if(samples[sampleIndex] == null || !recFilter.pass(record, samples[sampleIndex].split(","), vcfReader))
+ if( samples[i] == null || !recFilter.pass(record, samples[i].split(","), vcfReader))
return false;
}
- else // look at all samples
- {
- for(int i=0; i<samples.length; i++)
- {
- if( samples[i] == null || !recFilter.pass(record, samples[i].split(","), vcfReader))
- return false;
- }
- }
- break;
- case HeaderLine.FILTER_LINE: // FILTER
- break;
- case HeaderLine.FILTER_QUAL: // FILTER by quality score
- if( !recFilter.pass(record, new String[] { Float.toString(record.getQuality()) }, vcfReader))
- return false;
- break;
-
- case HeaderLine.FILTER_MULTALL_FLAG: // FILTER by quality score
- if( record.getAlt().isMultiAllele(sampleIndex) )
- return false;
- break;
- case HeaderLine.FILTER_NONSYN:
- if( !record.getAlt().isDeletion(vcfReader.isVcf_v4()) &&
- !record.getAlt().isInsertion(vcfReader.isVcf_v4()) &&
- record.getAlt().length() == 1 &&
- record.getRef().length() == 1)
- {
- short isSyn = record.getSynFlag(features, basePosition);
- if( (isSyn == 0 || isSyn == 2) )
- return false;
- }
- break;
- case HeaderLine.FILTER_SYN:
- if( !record.getAlt().isDeletion(vcfReader.isVcf_v4()) &&
- !record.getAlt().isInsertion(vcfReader.isVcf_v4()) &&
- record.getAlt().length() == 1 &&
- record.getRef().length() == 1)
- {
- short isSyn = record.getSynFlag(features, basePosition);
- if(isSyn == 1)
- return false;
- }
- default:
- break;
- }
+ }
+ break;
+ case HeaderLine.FILTER_LINE: // FILTER
+ break;
+ case HeaderLine.FILTER_QUAL: // FILTER by quality score
+ if( !recFilter.pass(record, new String[] { Float.toString(record.getQuality()) }, vcfReader))
+ return false;
+ break;
+
+ case HeaderLine.FILTER_MULTALL_FLAG: // FILTER by quality score
+ if( record.getAlt().isMultiAllele(sampleIndex) )
+ return false;
+ break;
+ case HeaderLine.FILTER_NONSYN:
+ if( !record.getAlt().isDeletion(vcfReader.isVcf_v4()) &&
+ !record.getAlt().isInsertion(vcfReader.isVcf_v4()) &&
+ record.getAlt().length() == 1 &&
+ record.getRef().length() == 1)
+ {
+ short isSyn = record.getSynFlag(features, basePosition);
+ if( (isSyn == 0 || isSyn == 2) )
+ return false;
+ }
+ break;
+ case HeaderLine.FILTER_SYN:
+ if( !record.getAlt().isDeletion(vcfReader.isVcf_v4()) &&
+ !record.getAlt().isInsertion(vcfReader.isVcf_v4()) &&
+ record.getAlt().length() == 1 &&
+ record.getRef().length() == 1)
+ {
+ short isSyn = record.getSynFlag(features, basePosition);
+ if(isSyn == 1)
+ return false;
+ }
+ default:
+ break;
}
- return true;
}
-
+ return true;
+
/* try
{
if(VCFFilter.MIN_DP > 0 && Integer.parseInt(record.getInfoValue("DP")) < VCFFilter.MIN_DP)