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gatk-3.8
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making my last commit message actually true 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4636 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2010-11-07 18:26:23 +00:00
parent be499fc986
commit 97db593efb
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
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@ -28,7 +28,7 @@ public class RMDIndexer extends CommandLineProgram {
@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)
@Input(fullName = "referenceSequence", shortName = "R", doc = "The reference to use when indexing; this sequence will be set in the index", required = false)
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)
@ -61,7 +61,7 @@ public class RMDIndexer extends CommandLineProgram {
+ 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 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()));