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better error catching, as well as allowing for default index naming, <filename>.idx 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4633 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-11-06 19:12:19 +00:00
parent cb2e26a004
commit 2a8c97a4a7
1 changed files with 9 additions and 4 deletions
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13
java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
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@ -3,6 +3,7 @@ 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;
@ -40,10 +41,6 @@ public class RMDIndexer extends CommandLineProgram {
@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
// ---------------------------------------------------------------------------------
@ -56,11 +53,19 @@ public class RMDIndexer extends CommandLineProgram {
// create a reference file reader
IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(referenceFile);
// 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.getAbsolutePath()));
logger.info(String.format("using type: %s", inputFileType));
logger.info(String.format("writing to location: %s", indexFile.getAbsolutePath()));
// try to index the file
// ---------------------------------------------------------------------------------