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fixing bug with fastq extension 

* PPP only recognized .fasta and .fq, failing when the user provided a .fastq file. Fixed.
This commit is contained in:
Mauricio Carneiro 2012-01-24 10:59:25 -05:00
parent 0a3172a9f1
commit 7c7ca0d799
1 changed files with 5 additions and 2 deletions
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7
public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
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@ -45,9 +45,12 @@ object QScriptUtils {
* to have empty lines and comment lines (lines starting with #). * to have empty lines and comment lines (lines starting with #).
*/ */
def createSeqFromFile(in: File):Seq[File] = { 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. // 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) return Seq(in)
var list: Seq[File] = Seq() var list: Seq[File] = Seq()