by request, an indexer tool to create Tribble style indexes outside of the GATK

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4632 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java

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+package org.broadinstitute.sting.gatk.refdata.indexer;
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.apache.log4j.Logger;
+import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.index.Index;
+import org.broad.tribble.index.IndexFactory;
+import org.broad.tribble.util.LittleEndianOutputStream;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
+import org.broadinstitute.sting.utils.Utils;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.Map;
+
+/**
+ * a utility class that can create an index, written to a target location.  This is useful when you're unable to write to the directory
+ * in which an index is located, or if you'd like to pre-index files to save time.
+ */
+public class RMDIndexer extends CommandLineProgram {
+    @Argument(shortName="in", fullName="inputFile", doc="The reference meta data file to index", required = true)
+    File inputFileSource = null;
+
+    @Argument(shortName="t", fullName="type", doc="The reference meta data file format (e.g. vcf, bed)", required = true)
+    String inputFileType = null;
+
+    @Input(fullName = "referenceSequence", shortName = "R", doc = "The reference to use when indexing; this sequence will be set in the index", required = true)
+    public File referenceFile = null;
+
+    @Input(shortName = "i", fullName = "indexFile", doc = "Where to write the index to (as a file), if not supplied we write to <inputFile>.idx", required = false)
+    public File indexFile = null;
+
+    @Argument(shortName = "ba", fullName = "balanceApproach", doc="the index balancing approach to take", required=false)
+    IndexFactory.IndexBalanceApproach approach = IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME;
+
+    private static Logger logger = Logger.getLogger(RMDIndexer.class);
+
+    @Override
+    protected int execute() throws Exception {
+        logger.info(String.format("attempting to index file:   %s",inputFileSource));
+        logger.info(String.format("using reference:            %s",referenceFile.getAbsolutePath()));
+        logger.info(String.format("using type:                 %s",inputFileType));
+        logger.info(String.format("writing to location:        %s",indexFile.getAbsolutePath()));
+
+        // check parameters
+        // ---------------------------------------------------------------------------------
+
+        // check the input parameters
+        if (referenceFile == null || !referenceFile.canRead())
+            throw new IllegalArgumentException("We can't read the reference file: "
+                + referenceFile + ", check that it exists, and that you have permissions to read it");
+
+        // create a reference file reader
+        IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(referenceFile);
+
+        // check that we can create the output file
+        if (indexFile == null || indexFile.exists())
+            throw new IllegalArgumentException("We can't write to the index file location: "
+                + indexFile + ", the index exists");
+
+
+        // try to index the file
+        // ---------------------------------------------------------------------------------
+
+        // get a track builder
+        RMDTrackBuilder builder = new RMDTrackBuilder();
+
+        // find the types available to the track builders
+        Map<String,Class> typeMapping = builder.getAvailableTrackNamesAndTypes();
+
+        // check that the type is valid
+        if (!typeMapping.containsKey(inputFileType))
+            throw new IllegalArgumentException("The type specified " + inputFileType + " is not a valid type.  Valid type list: " + Utils.join(",",typeMapping.keySet()));
+
+        // create the codec
+        FeatureCodec codec = builder.createByType(typeMapping.get(inputFileType));
+
+        // get some timing info
+        long currentTime = System.currentTimeMillis();
+
+        Index index = IndexFactory.createIndex(inputFileSource, codec, approach);
+
+        // create the output stream, and write the index
+        LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile));
+        index.write(stream);
+        stream.close();
+
+        // report and exit
+        logger.info("Successfully wrote the index to location: " + indexFile + " in " + ((System.currentTimeMillis() - currentTime)/1000) + " seconds");
+        return 0;  // return successfully
+    }
+
+
+    /**
+     * the generic call execute main
+     * @param argv the arguments from the command line
+     */
+    public static void main(String[] argv) {
+        try {
+            RMDIndexer instance = new RMDIndexer();
+            start(instance, argv);
+            System.exit(CommandLineProgram.result);
+        } catch (Exception e) {
+            exitSystemWithError(e);
+        }
+    }
+}

packages/RMDIndexer.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<package name="RMDIndexer">
+  <executable name="RMDIndexer">
+    <main-class name="org.broadinstitute.sting.gatk.refdata.indexer.RMDIndexer" />
+    <resource-bundle file="StingText.properties" />
+    <dependencies>
+      <package name="org.broad.tribble.*" />
+      <!-- the class itself -->
+      <class name="org.broadinstitute.sting.gatk.refdata.indexer.RMDIndexer" />
+    </dependencies>
+  </executable>
+</package>