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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 org.broad.tribble.FeatureCodec;
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.GATKFeature;
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
// our feature reader - allows queries
private BasicFeatureSource reader;
private FeatureSource reader;
// our sequence dictionary, which can be null
private final SAMSequenceDictionary dictionary;
@ -102,7 +101,7 @@ public class RMDTrack {
* @param dict the sam sequence dictionary
* @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.recordType = codec.getFeatureType();
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.IndexFactory;
import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.source.CachingFeatureSource;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
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 {
// 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");
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
* @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);
}
@ -143,8 +144,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the input file to create the track from (of the codec type)
* @return the FeatureReader instance
*/
public Pair<BasicFeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, String name, File inputFile) {
Pair<BasicFeatureSource, SAMSequenceDictionary> pair;
public Pair<FeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, String name, File inputFile) {
Pair<FeatureSource, SAMSequenceDictionary> pair;
if (inputFile.getAbsolutePath().endsWith(".gz"))
pair = createBasicFeatureSourceNoAssumedIndex(targetClass, name, inputFile);
else
@ -162,11 +163,11 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the file to load
* @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
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
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) {
throw new UserException(e.getMessage(), e);
}
@ -192,8 +193,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param inputFile the tribble file to parse
* @return the input file as a FeatureReader
*/
private Pair<BasicFeatureSource, SAMSequenceDictionary> getFeatureSource(Class targetClass, String name, File inputFile) {
Pair<BasicFeatureSource, SAMSequenceDictionary> reader;
private Pair<FeatureSource, SAMSequenceDictionary> getFeatureSource(Class targetClass, String name, File inputFile) {
Pair<FeatureSource, SAMSequenceDictionary> reader;
try {
Index index = loadIndex(inputFile, createCodec(targetClass, name));
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);
dictFromIndex = getSequenceDictionaryFromProperties(index);
}
reader = new Pair<BasicFeatureSource, SAMSequenceDictionary>(new BasicFeatureSource(inputFile.getAbsolutePath(),
index,
createCodec(targetClass, name)),
dictFromIndex);
FeatureSource source = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(targetClass, name));
//source = new CachingFeatureSource(source, 100, 100000);
reader = new Pair<FeatureSource, SAMSequenceDictionary>(source, dictFromIndex);
} catch (TribbleException e) {
throw new UserException(e.getMessage());
} catch (IOException e) {

8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
View File

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

6
java/src/org/broadinstitute/sting/utils/text/XReadLines.java
View File

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