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Removing this command-line tool. Purposely not doing this in stable so that users who may still use it have time to find other options. But the docs are no longer on the wiki.

This commit is contained in:
Eric Banks 2011-09-28 13:18:32 -04:00
parent 1f0e354fae
commit 1b45f21774
1 changed files with 0 additions and 130 deletions
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130
public/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.Tribble;
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.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import java.io.File;
import java.io.FileOutputStream;
/**
* 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);
private IndexedFastaSequenceFile ref = null;
private GenomeLocParser genomeLocParser = null;
@Override
protected int execute() throws Exception {
// 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");
// set the index file to the default name if they didn't specify a file
if (indexFile == null && inputFileSource != null)
indexFile = new File(inputFileSource.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION);
// 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");
logger.info(String.format("attempting to index file: %s", inputFileSource));
logger.info(String.format("using reference: %s", ((referenceFile != null) ? referenceFile.getAbsolutePath() : "(not supplied)")));
logger.info(String.format("using type: %s", inputFileType));
logger.info(String.format("writing to location: %s", indexFile.getAbsolutePath()));
// try to index the file
// ---------------------------------------------------------------------------------
// setup the reference
ref = new CachingIndexedFastaSequenceFile(referenceFile);
genomeLocParser = new GenomeLocParser(ref);
// get a track builder
RMDTrackBuilder builder = new RMDTrackBuilder(ref.getSequenceDictionary(),genomeLocParser, ValidationExclusion.TYPE.ALL);
// find the types available to the track builders
FeatureManager.FeatureDescriptor descriptor = builder.getFeatureManager().getByName(inputFileType);
// check that the type is valid
if (descriptor == null)
throw new IllegalArgumentException("The type specified " + inputFileType + " is not a valid type. Valid type list: " + builder.getFeatureManager().userFriendlyListOfAvailableFeatures());
// create the codec
FeatureCodec codec = builder.getFeatureManager().createCodec(descriptor, "foo", genomeLocParser);
// check if it's a reference dependent feature codec
if (codec instanceof ReferenceDependentFeatureCodec)
((ReferenceDependentFeatureCodec)codec).setGenomeLocParser(genomeLocParser);
// get some timing info
long currentTime = System.currentTimeMillis();
Index index = IndexFactory.createIndex(inputFileSource, codec, approach);
// add writing of the sequence dictionary, if supplied
builder.validateAndUpdateIndexSequenceDictionary(inputFileSource, index, ref.getSequenceDictionary());
// 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);
}
}
}