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RefMetaDataTracker no longer automagically converts inputs to VariantContexts 

This was no longer working properly given that DBSNP indels needed to be moved around.  The adaptor system is being refactored and you will need to convert files from X -> VCF for many tools to work.
This commit is contained in:
Mark DePristo 2011-08-01 15:21:16 -04:00
parent 8b1adb8c95
commit 184030dd56
1 changed files with 12 additions and 37 deletions
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49
public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
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@ -54,37 +54,12 @@ public class RefMetaDataTracker {
else {
map = new HashMap<String, RODRecordList>(allBindings.size());
for ( RODRecordList rod : allBindings ) {
//logger.debug(String.format("Binding %s to %s", name, rod));
if ( rod != null )
map.put(canonicalName(rod.getName()), maybeConvertToVariantContext(rod));
map.put(canonicalName(rod.getName()), rod);
}
}
}
/**
* A private converter that transforms a RODRecordList of objects of type X into
* a list of VariantContexts, if possible.
*
* TODO: should be removed when Features like dbsnp and hapmap produce VCs directly
*
* @param bindings
* @return
*/
private final RODRecordList maybeConvertToVariantContext(RODRecordList bindings) {
List<GATKFeature> values = new ArrayList<GATKFeature>(bindings.size());
for ( GATKFeature rec : bindings ) {
if ( VariantContextAdaptors.canBeConvertedToVariantContext(rec.getUnderlyingObject()) ) {
final VariantContext vc = VariantContextAdaptors.toVariantContext(bindings.getName(), rec.getUnderlyingObject(), ref);
if ( vc != null ) // it's possible that the conversion failed, but we continue along anyway
values.add(new GATKFeature.TribbleGATKFeature(ref.getGenomeLocParser(), vc, rec.getName()));
} else
values.add(rec);
}
return new RODRecordListImpl(bindings.getName(), values, bindings.getLocation());
}
// ------------------------------------------------------------------------------------------
//
//
@ -294,11 +269,11 @@ public class RefMetaDataTracker {
// ------------------------------------------------------------------------------------------
private <T extends Feature> List<T> addValues(final Collection<String> names,
final Class<T> type,
final List<T> values,
final GenomeLoc curLocation,
final boolean requireStartHere,
final boolean takeFirstOnly ) {
final Class<T> type,
final List<T> values,
final GenomeLoc curLocation,
final boolean requireStartHere,
final boolean takeFirstOnly ) {
for ( String name : names ) {
RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match
addValues(name, type, values, rodList, curLocation, requireStartHere, takeFirstOnly );
@ -308,12 +283,12 @@ public class RefMetaDataTracker {
}
private <T extends Feature> List<T> addValues(final String name,
final Class<T> type,
final List<T> values,
final RODRecordList rodList,
final GenomeLoc curLocation,
final boolean requireStartHere,
final boolean takeFirstOnly ) {
final Class<T> type,
final List<T> values,
final RODRecordList rodList,
final GenomeLoc curLocation,
final boolean requireStartHere,
final boolean takeFirstOnly ) {
for ( GATKFeature rec : rodList ) {
if ( ! requireStartHere || rec.getLocation().getStart() == curLocation.getStart() ) { // ok, we are going to keep this thing
Object obj = rec.getUnderlyingObject();