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Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1

This commit is contained in:
Mark Fleharty 2015-11-20 11:23:02 -05:00
parent 29e86a0d01
commit 1443ee8c7f
1 changed files with 1 additions and 1 deletions
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2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
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@ -292,7 +292,7 @@ public class BQSRIntegrationTest extends WalkerTest {
" -R " + hg18Reference + " -R " + hg18Reference +
" -I " + HiSeqBam + " -I " + HiSeqBam +
" -L " + HiSeqInterval + " -L " + HiSeqInterval +
" -SQQ 4 -q1 4 " + " -SQQ 4 -ql 4 " +
" -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" + " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
" -o /dev/null", " -o /dev/null",
0, 0,