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GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4525 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-10-20 00:29:02 +00:00
parent 7a291a8ff3
commit f7ce18553e
4 changed files with 21 additions and 24 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
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@ -27,7 +27,6 @@ import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource; import org.broad.tribble.FeatureSource;
import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -55,7 +54,7 @@ public class RMDTrack {
private final File file; // the associated file we create the reader from private final File file; // the associated file we create the reader from
// our feature reader - allows queries // our feature reader - allows queries
private BasicFeatureSource reader; private FeatureSource reader;
// our sequence dictionary, which can be null // our sequence dictionary, which can be null
private final SAMSequenceDictionary dictionary; private final SAMSequenceDictionary dictionary;
@ -102,7 +101,7 @@ public class RMDTrack {
* @param dict the sam sequence dictionary * @param dict the sam sequence dictionary
* @param codec the feature codec we use to decode this type * @param codec the feature codec we use to decode this type
*/ */
public RMDTrack(Class type, String name, File file, BasicFeatureSource reader, SAMSequenceDictionary dict, FeatureCodec codec) { public RMDTrack(Class type, String name, File file, FeatureSource reader, SAMSequenceDictionary dict, FeatureCodec codec) {
this.type = type; this.type = type;
this.recordType = codec.getFeatureType(); this.recordType = codec.getFeatureType();
this.name = name; this.name = name;

26
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -32,6 +32,7 @@ import org.broad.tribble.*;
import org.broad.tribble.index.Index; import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.source.CachingFeatureSource;
import org.broad.tribble.util.LittleEndianOutputStream; import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
@ -121,7 +122,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
*/ */
public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException { public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException {
// return a feature reader track // return a feature reader track
Pair<BasicFeatureSource, SAMSequenceDictionary> pair = createFeatureReader(targetClass, name, inputFile); Pair<FeatureSource, SAMSequenceDictionary> pair = createFeatureReader(targetClass, name, inputFile);
if (pair == null) throw new UserException.CouldNotReadInputFile(inputFile, "Unable to make the feature reader for input file"); if (pair == null) throw new UserException.CouldNotReadInputFile(inputFile, "Unable to make the feature reader for input file");
return new RMDTrack(targetClass, name, inputFile, pair.first, pair.second, createCodec(targetClass, name)); return new RMDTrack(targetClass, name, inputFile, pair.first, pair.second, createCodec(targetClass, name));
} }
@ -132,7 +133,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the input file, that corresponds to the feature type * @param inputFile the input file, that corresponds to the feature type
* @return a pair of <BasicFeatureSource, SAMSequenceDictionary> * @return a pair of <BasicFeatureSource, SAMSequenceDictionary>
*/ */
public Pair<BasicFeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, File inputFile) { public Pair<FeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, File inputFile) {
return createFeatureReader(targetClass, "anonymous", inputFile); return createFeatureReader(targetClass, "anonymous", inputFile);
} }
@ -143,8 +144,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the input file to create the track from (of the codec type) * @param inputFile the input file to create the track from (of the codec type)
* @return the FeatureReader instance * @return the FeatureReader instance
*/ */
public Pair<BasicFeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, String name, File inputFile) { public Pair<FeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, String name, File inputFile) {
Pair<BasicFeatureSource, SAMSequenceDictionary> pair; Pair<FeatureSource, SAMSequenceDictionary> pair;
if (inputFile.getAbsolutePath().endsWith(".gz")) if (inputFile.getAbsolutePath().endsWith(".gz"))
pair = createBasicFeatureSourceNoAssumedIndex(targetClass, name, inputFile); pair = createBasicFeatureSourceNoAssumedIndex(targetClass, name, inputFile);
else else
@ -162,11 +163,11 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the file to load * @param inputFile the file to load
* @return a feature reader implementation * @return a feature reader implementation
*/ */
private Pair<BasicFeatureSource, SAMSequenceDictionary> createBasicFeatureSourceNoAssumedIndex(Class targetClass, String name, File inputFile) { private Pair<FeatureSource, SAMSequenceDictionary> createBasicFeatureSourceNoAssumedIndex(Class targetClass, String name, File inputFile) {
// we might not know the index type, try loading with the default reader constructor // we might not know the index type, try loading with the default reader constructor
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file"); logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try { try {
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null); return new Pair<FeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
} catch (TribbleException e) { } catch (TribbleException e) {
throw new UserException(e.getMessage(), e); throw new UserException(e.getMessage(), e);
} }
@ -192,8 +193,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the tribble file to parse * @param inputFile the tribble file to parse
* @return the input file as a FeatureReader * @return the input file as a FeatureReader
*/ */
private Pair<BasicFeatureSource, SAMSequenceDictionary> getFeatureSource(Class targetClass, String name, File inputFile) { private Pair<FeatureSource, SAMSequenceDictionary> getFeatureSource(Class targetClass, String name, File inputFile) {
Pair<BasicFeatureSource, SAMSequenceDictionary> reader; Pair<FeatureSource, SAMSequenceDictionary> reader;
try { try {
Index index = loadIndex(inputFile, createCodec(targetClass, name)); Index index = loadIndex(inputFile, createCodec(targetClass, name));
try { logger.info(String.format(" Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); } try { logger.info(String.format(" Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); }
@ -207,11 +208,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
setIndexSequenceDictionary(index,dict,indexFile,true); setIndexSequenceDictionary(index,dict,indexFile,true);
dictFromIndex = getSequenceDictionaryFromProperties(index); dictFromIndex = getSequenceDictionaryFromProperties(index);
} }
reader = new Pair<BasicFeatureSource, SAMSequenceDictionary>(new BasicFeatureSource(inputFile.getAbsolutePath(), FeatureSource source = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(targetClass, name));
index, //source = new CachingFeatureSource(source, 100, 100000);
createCodec(targetClass, name)), reader = new Pair<FeatureSource, SAMSequenceDictionary>(source, dictFromIndex);
dictFromIndex);
} catch (TribbleException e) { } catch (TribbleException e) {
throw new UserException(e.getMessage()); throw new UserException(e.getMessage());
} catch (IOException e) { } catch (IOException e) {

8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -312,10 +312,10 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
} else { } else {
truth = validation.getGenotype(sample).getType(); truth = validation.getGenotype(sample).getType();
// interesting = "ConcordanceStatus=FP"; // interesting = "ConcordanceStatus=FP";
if (discordantInteresting && truth.ordinal() != called.ordinal()) if (discordantInteresting && truth.ordinal() != called.ordinal())
{ {
interesting = "ConcordanceStatus=" + truth.ordinal() + "/" + called.ordinal(); interesting = "ConcordanceStatus=" + truth + "/" + called;
} }
} }
sampleStats.incrValue(sample, truth, called); sampleStats.incrValue(sample, truth, called);

6
java/src/org/broadinstitute/sting/utils/text/XReadLines.java
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@ -84,9 +84,8 @@ public class XReadLines implements Iterator<String>, Iterable<String> {
* Creates a new xReadLines object to read lines from an input stream * Creates a new xReadLines object to read lines from an input stream
* *
* @param inputStream * @param inputStream
* @throws FileNotFoundException
*/ */
public XReadLines(final InputStream inputStream, final boolean trimWhitespace) throws FileNotFoundException { public XReadLines(final InputStream inputStream, final boolean trimWhitespace) {
this(new BufferedReader(new InputStreamReader(inputStream)), trimWhitespace); this(new BufferedReader(new InputStreamReader(inputStream)), trimWhitespace);
} }
@ -99,9 +98,8 @@ public class XReadLines implements Iterator<String>, Iterable<String> {
* Creates a new xReadLines object to read lines from an bufferedReader * Creates a new xReadLines object to read lines from an bufferedReader
* *
* @param reader * @param reader
* @throws FileNotFoundException
*/ */
public XReadLines(final BufferedReader reader, final boolean trimWhitespace) throws FileNotFoundException { public XReadLines(final BufferedReader reader, final boolean trimWhitespace) {
try { try {
this.in = reader; this.in = reader;
nextline = readNextLine(); nextline = readNextLine();