Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest

Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-23 17:08:30 -05:00 · 2015-11-23 17:08:30 -05:00 · 5a3756410c
parent b0730c2b81 1443ee8c7f
commit 5a3756410c
1 changed files with 1 additions and 1 deletions
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
@ -292,7 +292,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                        " -R " + hg18Reference +
                        " -I " + HiSeqBam +
                        " -L " + HiSeqInterval +
-                        " -SQQ 4 -q1 4 " +
+                        " -SQQ 4 -ql 4 " +
                        " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
                        " -o /dev/null",
                0,