From f46f7d9b23d22ac249fddbfacc4e748b61940ac9 Mon Sep 17 00:00:00 2001 From: James Warren Date: Fri, 14 Jun 2013 14:25:16 -0700 Subject: [PATCH] deducing dictionary path should not use global find and replace Signed-off-by: David Roazen --- .../sting/gatk/datasources/reference/ReferenceDataSource.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index 01edd44ba..edd3d324c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -68,8 +68,8 @@ public class ReferenceDataSource { final File indexFile = new File(fastaFile.getAbsolutePath() + ".fai"); // determine the name for the dict file - final String fastaExt = fastaFile.getAbsolutePath().endsWith("fa") ? ".fa" : ".fasta"; - final File dictFile = new File(fastaFile.getAbsolutePath().replace(fastaExt, ".dict")); + final String fastaExt = fastaFile.getAbsolutePath().endsWith("fa") ? "\\.fa$" : "\\.fasta$"; + final File dictFile = new File(fastaFile.getAbsolutePath().replaceAll(fastaExt, ".dict")); // It's an error if either the fai or dict file does not exist. The user is now responsible // for creating these files.