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Add integration test for quartiles overflowing on interval reduce 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-08 16:18:45 +00:00
parent 21bf8b4b93
commit bca9bdcc68
1 changed files with 27 additions and 2 deletions
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29
java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java
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@ -53,19 +53,44 @@ public class CoverageStatisticsIntegrationTest extends WalkerTest {
String[] intervals = {"1:10,000,000-10,000,800","1:10,250,001-10,250,500","1:10,500,001-10,500,300","1:10,750,001-10,750,400"};
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam","/broad/1KG/DCC_merged/freeze5/NA19240.pilot2.454.bam"};
String cmd = buildRootCmd(b36,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts";
String cmd = buildRootCmd(b36,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -both";
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
// now add the expected files that get generated
spec.addAuxFile("cb87d6069ac60c73f047efc6d9386619", baseOutputFile);
spec.addAuxFile("959937a9b0ace520b4b7d9915d708003", baseOutputFile);
spec.addAuxFile("aff2349d6dc221c08f6c469379aeaedf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("6476ed0c54a4307a618aa6d3268b050f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("c744a298b7541f3f823e6937e9a0bc67", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics"));
spec.addAuxFile("65318c1e73d98a59cc6f817cde12d3d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary_statistics"));
spec.addAuxFile("9fc19f773a7ddfbb473d124e675a3d94", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("223377e07b35e81a394b75b38d8e72ee", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("096f4ed94020327288ea76245ebd6942", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("437b92f70a6c414de9178a12c02511c2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics"));
spec.addAuxFile("cf1d038e278f28f382f79c30d8416b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("a374410efe20609c5c4b87a6da7f4d51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
execute("testBaseOutputNoFiltering",spec);
}
@Test
public void testMedianOverRightHandBin() {
File base = this.createTempFile("depthofcoveragelowbins",".tmp");
this.setOutputFileLocation(base);
String[] intervals = {"1:10,000,000-10,000,800","1:10,250,001-10,250,500","1:10,500,001-10,500,300","1:10,750,001-10,750,400"};
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam","/broad/1KG/DCC_merged/freeze5/NA19240.pilot2.454.bam"};
String cmd = buildRootCmd(b36,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) +
" -mmq 0 -mbq 0 -dels -baseCounts -both --start 1 --stop 14 --nBins 13";
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
spec.addAuxFile("959937a9b0ace520b4b7d9915d708003", base);
spec.addAuxFile("219d643627eedd696bc476aac96376c2", createTempFileFromBase(base.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("dd0225cf1e0b0bd4289b82fd4939f9fd", createTempFileFromBase(base.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("63575a8a2110507e08d421d44d06b327", createTempFileFromBase(base.getAbsolutePath()+".sample_interval_summary"));
execute("testMedianOverRHBin",spec);
}
public File createTempFileFromBase(String name) {
File fl = new File(name);
fl.deleteOnExit();