From 7c7ca0d799256c484fa65ded9e1f2c04585c761f Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 24 Jan 2012 10:59:25 -0500 Subject: [PATCH] fixing bug with fastq extension * PPP only recognized .fasta and .fq, failing when the user provided a .fastq file. Fixed. --- .../org/broadinstitute/sting/queue/util/QScriptUtils.scala | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala index 5d76f39ed..1529d9951 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala @@ -45,9 +45,12 @@ object QScriptUtils { * to have empty lines and comment lines (lines starting with #). */ def createSeqFromFile(in: File):Seq[File] = { - // If the file provided ends with .bam, .fasta or .fq, it is not a bam list, we treat it as a single file. + // If the file provided ends with .bam, .fasta, fastq or .fq, it is not a bam list, we treat it as a single file. // and return a list with only this file. - if (in.toString.endsWith(".bam") || in.toString.endsWith(".fasta") || in.toString.endsWith(".fq")) + if (in.toString.toUpperCase.endsWith(".BAM") || + in.toString.toUpperCase.endsWith(".FASTA") || + in.toString.toUpperCase.endsWith(".FQ") || + in.toString.toUpperCase.endsWith("FASTQ") ) return Seq(in) var list: Seq[File] = Seq()