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

Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser 

Updated all walkers that used the now deleted methods.
This commit is contained in:
Mark DePristo 2011-08-03 16:04:51 -04:00
parent f6563c0f9f
commit 800bb97f0b
3 changed files with 92 additions and 53 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

114
public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
View File

@ -56,7 +56,7 @@ public class RefMetaDataTracker {
else {
Map<String, RODRecordList> tmap = new HashMap<String, RODRecordList>(allBindings.size());
for ( RODRecordList rod : allBindings ) {
if ( rod != null )
if ( rod != null && ! rod.isEmpty() )
tmap.put(canonicalName(rod.getName()), rod);
}
@ -141,17 +141,37 @@ public class RefMetaDataTracker {
@Requires({"type != null", "onlyAtThisLoc != null"})
public <T extends Feature> T getFirstValue(final Class<T> type, final GenomeLoc onlyAtThisLoc) {
return safeGetFirst(getValues(type, onlyAtThisLoc));
}
//
// ROD binding accessors
//
/**
* Gets all of the Tribble features bound to RodBinding spanning this locus, returning them as
* a list of specific type T extending Feature.
*
* Note that this function assumes that all of the bound features are instances of or
* subclasses of T. A ClassCastException will occur if this isn't the case.
*
* @param rodBinding Only Features coming from the track associated with this rodBinding are fetched
* @param <T> The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features
* @return A freshly allocated list of all of the bindings, or an empty list if none are bound.
*/
@Requires({"rodBinding != null"})
@Ensures("result != null")
public <T extends Feature> List<T> getValues(final RodBinding<T> rodBinding) {
return addValues(rodBinding.getName(), rodBinding.getType(), new ArrayList<T>(1), getTrackDataByName(rodBinding), null, false, false);
}
/**
* Gets all of the Tribble features bound to any RodBinding in rodBindings,
* spanning this locus, returning them as a list of specific type T extending Feature.
*
* Note that this function assumes that all of the bound features are instances of or
* subclasses of T. A ClassCastException will occur if this isn't the case.
*
* @param rodBindings Only Features coming from the tracks associated with one of rodBindings are fetched
* @param <T> The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features
* @return A freshly allocated list of all of the bindings, or an empty list if none are bound.
*/
@Requires({"rodBindings != null"})
@Ensures("result != null")
public <T extends Feature> List<T> getValues(final Collection<RodBinding<T>> rodBindings) {
@ -161,12 +181,28 @@ public class RefMetaDataTracker {
return results;
}
/**
* The same logic as @link #getValues(RodBinding) but enforces that each Feature start at onlyAtThisLoc
*
* @param rodBinding Only Features coming from the track associated with this rodBinding are fetched
* @param <T> The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features
* @param onlyAtThisLoc only Features starting at this site are considered
* @return A freshly allocated list of all of the bindings, or an empty list if none are bound.
*/
@Requires({"rodBinding != null", "onlyAtThisLoc != null"})
@Ensures("result != null")
public <T extends Feature> List<T> getValues(final RodBinding<T> rodBinding, final GenomeLoc onlyAtThisLoc) {
return addValues(rodBinding.getName(), rodBinding.getType(), new ArrayList<T>(1), getTrackDataByName(rodBinding), onlyAtThisLoc, true, false);
}
/**
* The same logic as @link #getValues(List) but enforces that each Feature start at onlyAtThisLoc
*
* @param rodBindings Only Features coming from the tracks associated with one of rodBindings are fetched
* @param <T> The Tribble Feature type of the rodBinding, and consequently the type of the resulting list of Features
* @param onlyAtThisLoc only Features starting at this site are considered
* @return A freshly allocated list of all of the bindings, or an empty list if none are bound.
*/
@Requires({"rodBindings != null", "onlyAtThisLoc != null"})
@Ensures("result != null")
public <T extends Feature> List<T> getValues(final Collection<RodBinding<T>> rodBindings, final GenomeLoc onlyAtThisLoc) {
@ -176,16 +212,44 @@ public class RefMetaDataTracker {
return results;
}
/**
* Uses the same logic as @getValues(RodBinding) to determine the list
* of eligible Features and select a single element from the resulting set
* of eligible features.
*
* @param rodBinding Only Features coming from the track associated with this rodBinding are fetched
* @param <T> as above
* @return A random single element the eligible Features found, or null if none are bound.
*/
@Requires({"rodBinding != null"})
public <T extends Feature> T getFirstValue(final RodBinding<T> rodBinding) {
return safeGetFirst(addValues(rodBinding.getName(), rodBinding.getType(), null, getTrackDataByName(rodBinding), null, false, true));
}
/**
* Uses the same logic as @getValues(RodBinding, GenomeLoc) to determine the list
* of eligible Features and select a single element from the resulting set
* of eligible features.
*
* @param rodBinding Only Features coming from the track associated with this rodBinding are fetched
* @param <T> as above
* @param onlyAtThisLoc only Features starting at this site are considered
* @return A random single element the eligible Features found, or null if none are bound.
*/
@Requires({"rodBinding != null", "onlyAtThisLoc != null"})
public <T extends Feature> T getFirstValue(final RodBinding<T> rodBinding, final GenomeLoc onlyAtThisLoc) {
return safeGetFirst(addValues(rodBinding.getName(), rodBinding.getType(), null, getTrackDataByName(rodBinding), onlyAtThisLoc, true, true));
}
/**
* Uses the same logic as @getValues(List) to determine the list
* of eligible Features and select a single element from the resulting set
* of eligible features.
*
* @param rodBindings Only Features coming from the tracks associated with these rodBindings are fetched
* @param <T> as above
* @return A random single element the eligible Features found, or null if none are bound.
*/
@Requires({"rodBindings != null"})
public <T extends Feature> T getFirstValue(final Collection<RodBinding<T>> rodBindings) {
for ( RodBinding<T> rodBinding : rodBindings ) {
@ -196,6 +260,16 @@ public class RefMetaDataTracker {
return null;
}
/**
* Uses the same logic as @getValues(RodBinding,GenomeLoc) to determine the list
* of eligible Features and select a single element from the resulting set
* of eligible features.
*
* @param rodBindings Only Features coming from the tracks associated with these rodBindings are fetched
* @param <T> as above
* @param onlyAtThisLoc only Features starting at this site are considered
* @return A random single element the eligible Features found, or null if none are bound.
*/
@Requires({"rodBindings != null", "onlyAtThisLoc != null"})
public <T extends Feature> T getFirstValue(final Collection<RodBinding<T>> rodBindings, final GenomeLoc onlyAtThisLoc) {
for ( RodBinding<T> rodBinding : rodBindings ) {
@ -275,24 +349,6 @@ public class RefMetaDataTracker {
return l;
}
@Deprecated
public List<GATKFeature> getValuesAsGATKFeatures(final RodBinding rodBinding) {
return getValuesAsGATKFeatures(rodBinding.getName());
}
/**
* get all the GATK features associated with a specific track name
* @param name the name of the track we're looking for
* @return a list of GATKFeatures for the target rmd
*
* Important: The list returned by this function is guaranteed not to be null, but may be empty!
*/
@Deprecated
public List<GATKFeature> getValuesAsGATKFeatures(final String name) {
return getTrackDataByName(name);
}
/**
* Get all of the RMD tracks at the current site. Each track is returned as a single compound
* object (RODRecordList) that may contain multiple RMD records associated with the current site.
@ -300,13 +356,7 @@ public class RefMetaDataTracker {
* @return List of all tracks
*/
public List<RODRecordList> getBoundRodTracks() {
LinkedList<RODRecordList> bound = new LinkedList<RODRecordList>();
for ( RODRecordList value : map.values() ) {
if ( value.size() != 0 ) bound.add(value);
}
return bound;
return new ArrayList<RODRecordList>(map.values());
}
/**
@ -361,10 +411,10 @@ public class RefMetaDataTracker {
values = addValues(name, type, values, rodList, curLocation, requireStartHere, takeFirstOnly );
if ( takeFirstOnly && ! values.isEmpty() )
break;
}
}
return values;
}
return values;
}

23
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -34,6 +34,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -443,6 +444,15 @@ public class GenomeLocParser {
}
}
/**
* Creates a GenomeLoc from a Tribble feature
* @param feature
* @return
*/
public GenomeLoc createGenomeLoc(final Feature feature) {
return createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
}
/**
* create a new genome loc, given the contig name, and a single position. Must be on the reference
*
@ -457,19 +467,6 @@ public class GenomeLocParser {
return createGenomeLoc(contig, getContigIndex(contig), pos, pos);
}
// /**
// * Creates a new GenomeLoc without performing any validation on its contig or bounds.
// * FOR UNIT TESTING PURPOSES ONLY!
// *
// * @param contig the contig name
// * @param start start position of the interval
// * @param stop stop position of the interval
// * @return a new GenomeLoc representing the specified location
// */
// public GenomeLoc createGenomeLocWithoutValidation( String contig, int start, int stop ) {
// return new GenomeLoc(contig, getContigIndexWithoutException(contig), start, stop);
// }
/**
* create a new genome loc from an existing loc, with a new start position
* Note that this function will NOT explicitly check the ending offset, in case someone wants to

8
public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
View File

@ -181,20 +181,12 @@ public class RefMetaDataTrackerUnitTest {
private <T> void testSimpleBindings(String name, RefMetaDataTracker tracker, RODRecordList expected) {
List<Feature> asValues = tracker.getValues(Feature.class, name);
List<GATKFeature> asFeatures = tracker.getValuesAsGATKFeatures(name);
Assert.assertEquals(tracker.hasValues(name), expected != null);
Assert.assertEquals(asFeatures.size(), expected == null ? 0 : expected.size());
Assert.assertEquals(asValues.size(), expected == null ? 0 : expected.size());
if ( expected != null ) {
for ( GATKFeature e : expected ) {
boolean foundFeature = false;
for ( GATKFeature f : asFeatures ) {
if ( e.getUnderlyingObject() == f.getUnderlyingObject() ) foundFeature = true;
}
Assert.assertTrue(foundFeature, "Never found expected GATKFeature " + e + " bound to " + name + " in " + tracker);
boolean foundValue = false;
for ( Feature f : asValues ) {
if ( e.getUnderlyingObject() == f ) foundValue = true;