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Updating tests to handle bad validation data files (that used the wrong qual score encoding); overrides push from stable.

This commit is contained in:
Eric Banks 2012-12-03 22:01:07 -05:00
parent 67932b357d
commit bca860723a
2 changed files with 4 additions and 2 deletions
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2
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -37,6 +37,7 @@ public class BQSRIntegrationTest extends WalkerTest {
" -L " + interval +
args +
" -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s";
}
@ -112,6 +113,7 @@ public class BQSRIntegrationTest extends WalkerTest {
" -R " + b36KGReference +
" -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" +
" -L 1:50,000-80,000" +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s",
1, // just one output file
UserException.class);

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -436,8 +436,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testNsInCigar() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
Arrays.asList("d6d40bacd540a41f305420dfea35e04a"));
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1,
Arrays.asList("32f18ba50406cd8c8069ba07f2f89558"));
executeTest("test calling on reads with Ns in CIGAR", spec);
}