example windowed ROD walker for Kristian, and updates to Tribble

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -52,6 +52,17 @@ import java.util.Map;
  *
  * This class keeps track of the available codecs, and knows how to put together a track of
  * that gets iterators from the FeatureReader using Tribble.
+ *
+ * Here's an example run command to find SNPs 200 base pairs up and downstream of the target file.
+ *
+ * java -jar dist/GenomeAnalysisTK.jar \
+ * -R /broad/1KG/reference/human_b36_both.fasta \
+ * -L 1:1863 \
+ * -L MT:16520 \
+ * -db /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b36.rod \
+ * -dbw 200 \
+ * -l INFO \
+ * -T DbSNPWindowCounter
  */
 public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implements RMDTrackBuilder {
     /**
@@ -92,6 +103,19 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
     public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException {
         // make a feature reader
         FeatureReader reader;
+        reader = createFeatureReader(targetClass, inputFile);
+        // return a feature reader track
+        return new FeatureReaderTrack(targetClass, name, inputFile, reader);
+    }
+
+    /**
+     * create a feature reader of the specified type
+     * @param targetClass the target codec type
+     * @param inputFile the input file to create the track from (of the codec type)
+     * @return the FeatureReader instance
+     */
+    public FeatureReader createFeatureReader(Class targetClass, File inputFile) {
+        FeatureReader reader = null;
         try {
             // check to see if the input file has an index
             if (requireIndex(inputFile)) {
@@ -107,8 +131,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
         } catch (IOException e) {
             throw new StingException("Unable to make the index file for " + inputFile, e);
         }
-        // return a feature reader track
-        return new FeatureReaderTrack(targetClass, name, inputFile, reader);
+        return reader;
     }
 
     /**
@@ -120,13 +143,13 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
      */
     public static LinearIndex createIndex(File inputFile, FeatureCodec codec) throws IOException {
         LinearIndexCreator create = new LinearIndexCreator(inputFile, codec);
-        create.setDisplayProgress(false);  // don't display progress indicators
-
+        
         // if we can write the index, we should, but if not just create it in memory
-        if (new File(inputFile.getAbsoluteFile() + linearIndexExtension).canWrite())
+        File indexFile = new File(inputFile.getAbsoluteFile() + linearIndexExtension);
+        if (indexFile.getParentFile().canWrite() && (!indexFile.exists() || indexFile.canWrite()))
             return create.createIndex();
         else {
-            logger.info("Unable to write to location " + inputFile.getAbsoluteFile() + linearIndexExtension + " for index file, creating index in memory only");
+            logger.info("Unable to write to location " + indexFile + " for index file, creating index in memory only");
             return create.createIndex(null);
         }
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DbSNPWindowCounter.java

@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.oneoffprojects.walkers;
+
+import org.broad.tribble.FeatureIterator;
+import org.broad.tribble.FeatureReader;
+import org.broad.tribble.dbsnp.DbSNPCodec;
+import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+/**
+ * DbSNPWindowCounter
+ *
+ * Count the number of upstream and downstream dbSNP entries from the current position using the specified window size.
+ * (really the window size upstream and downstream, so windowSize * 2)
+ *
+ * @Author Aaron
+ * @Date May 7th, 2010
+ */
+@By(DataSource.REFERENCE)
+@Requires({DataSource.REFERENCE, DataSource.REFERENCE_BASES})
+public class DbSNPWindowCounter extends LocusWalker<Integer, Long> {
+
+    // what we read in new tracks with
+    private FeatureReader reader;
+
+    @Argument(fullName = "dbSNPFile", shortName = "db", doc="The dbsnp file to search upstream and downstream for nearby snps", required = true)
+    private File myDbSNPFile;
+
+    @Argument(fullName = "dbSNPWindowSize", shortName = "dbw", doc="The distance to look both upstream and downstream for SNPs", required = true)
+    private int windowSize;
+
+
+    public void initialize() {
+        TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder();
+        reader = builder.createFeatureReader(DbSNPCodec.class,myDbSNPFile);
+    }
+
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        FeatureIterator<DbSNPFeature> dbSNPs;
+
+        // our upstream and downstream window locations
+        int windowStart = (int)Math.max(context.getLocation().getStart()-windowSize,0);
+        int windowStop  = (int)context.getLocation().getStop()+windowSize;
+
+        // query the dnSNP iterator
+        try {
+            dbSNPs = reader.query(context.getContig(),
+                    windowStart,
+                    windowStop);
+        } catch (IOException e) {
+            throw new StingException("Unable to query dbSNP track due to IO Exception",e);
+        }
+
+        // count the number of dbSNPs we've seen
+        int counter = 0;
+        for (DbSNPFeature feature: dbSNPs)
+            counter++;
+        out.println(context.getContig() + ":" + windowStart + "-" + context.getContig() + ":" + windowStop + "=" +
+                    counter + " (dnSNP records)");
+        return 1;
+    }
+
+    public Long reduceInit() { return 0l; }
+
+    public Long reduce(Integer value, Long sum) {
+        return value + sum;
+    }
+}

java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java

@@ -23,6 +23,7 @@
 
 package org.broadinstitute.sting.gatk.refdata.tracks.builders;
 
+
 import org.broad.tribble.vcf.VCFCodec;
 import org.broadinstitute.sting.BaseTest;
 import org.junit.Assert;

settings/repository/org.broad/tribble-77.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="77" status="integration" publication="20100504124200" />
-</ivy-module>

settings/repository/org.broad/tribble-79.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="79" status="integration" publication="20100507124200" />
+</ivy-module>