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another small bug with the file extension.

This commit is contained in:
Mauricio Carneiro 2012-01-24 16:13:53 -05:00
parent ffd61f4c1c
commit 97499529c7
1 changed files with 2 additions and 2 deletions
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4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -62,12 +62,12 @@ class PacbioProcessingPipeline extends QScript {
var USE_BWA: Boolean = false var USE_BWA: Boolean = false
var resetQuals: Boolean = true var resetQuals: Boolean = true
if (file.endsWith(".fasta") || file.endsWith(".fq")) { if (file.endsWith(".fasta") || file.endsWith(".fq") || file.endsWith(".fastq")) {
if (bwaPath == null) { if (bwaPath == null) {
throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA"); throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA");
} }
USE_BWA = true USE_BWA = true
if (file.endsWith(".fq")) if (file.endsWith(".fq") || file.endsWith(".fastq"))
resetQuals = false resetQuals = false
} }