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Added integration test for running the recalibrator with no index. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2393 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-17 19:10:53 +00:00
parent c75ec67f84
commit 07f1859290
1 changed files with 54 additions and 0 deletions
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54
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -163,4 +163,58 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "f5a0adce5458ab661029fa5056a55551" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
String md5 = entry.getValue();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R /broad/1KG/reference/human_b36_both.fasta" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -T CountCovariates" +
" -I " + bam +
" -cov ReadGroupCovariate" +
" -cov QualityScoreCovariate" +
" --sorted_output" +
" --solid_recal_mode DO_NOTHING" +
" -recalFile %s" +
" -U",
1, // just one output file
Arrays.asList(md5));
List<File> result = executeTest("testCountCovariatesNoIndex", spec).getFirst();
paramsFiles.put(bam, result.get(0).getAbsolutePath());
}
}
@Test
public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "dd8705b54f0ffbedb689608221ade13a" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
String md5 = entry.getValue();
String paramsFile = paramsFiles.get(bam);
System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
if ( paramsFile != null ) {
WalkerTestSpec spec = new WalkerTestSpec(
"-R /broad/1KG/reference/human_b36_both.fasta" +
" -T TableRecalibration" +
" -I " + bam +
" -outputBam %s" +
" --no_pg_tag" +
" --solid_recal_mode DO_NOTHING" +
" -recalFile " + paramsFile +
" -U",
1, // just one output file
Arrays.asList(md5));
executeTest("testTableRecalibratorNoIndex", spec);
}
}
}
}