From 97db593efbafb46f1aa145d3b9cf6873d8dc8e01 Mon Sep 17 00:00:00 2001 From: aaron Date: Sun, 7 Nov 2010 18:26:23 +0000 Subject: [PATCH] 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 --- .../broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java b/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java index 2b0d726a0..b4b267b98 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java @@ -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 .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()));