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Check in missing .tsv test cases.
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@cmnbroad
cmnbroad committed May 13, 2024
1 parent b4c1855 commit d3970e5
Showing 1 changed file with 31 additions and 17 deletions.
48 changes: 31 additions & 17 deletions src/test/java/org/broadinstitute/hellbender/CRAMIssue8768DetectorIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ public Object[][] getFileDiagnosticsTestCases() {
"src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/thisFileIsCorruptMito.false.bug8768.txt",
"src/test/resources/filediagnostics/thisFileIsCorruptMito.false.bug8768.tsv",
},
{
// test file created by rewriting the htsjdk test file
Expand All @@ -39,20 +40,23 @@ public Object[][] getFileDiagnosticsTestCases() {
"src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "true")),
"src/test/resources/filediagnostics/thisFileIsCorruptMito.true.bug8768.txt",
"src/test/resources/filediagnostics/thisFileIsCorruptMito.true.bug8768.tsv",
},
{
// 0 bad containers
NA12878_20_21_WGS_cram,
b37_reference_20_21,
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt",
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv",
},
{
// 0 bad containers
NA12878_20_21_WGS_cram,
b37_reference_20_21,
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "true")),
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt",
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv",
},
{
// test file created by rewriting the htsjdk test file
Expand All @@ -65,48 +69,58 @@ public Object[][] getFileDiagnosticsTestCases() {
"src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/thisFileIsCorruptMito.2BadContainers.false.bug8768.txt",
"src/test/resources/filediagnostics/thisFileIsCorruptMito.2BadContainers.false.bug8768.tsv",
},
{
// test file created by rewriting the htsjdk test file
// src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.cram using a version
// of GATK that has bug https://github.com/broadinstitute/gatk/issues/8768, along with code
// to force the file to have 2 bad containers by forcing numerous reads to be aligned to
// position 1.
// // 3 bad containers
"src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.bug8768.cram",
"src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.false.bug8768.txt",
// 3 bad containers
"src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.bug8768.cram",
"src/test/resources/filediagnostics/mitoCorrupt.bug8768.fa",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.false.bug8768.txt",
"src/test/resources/filediagnostics/thisFileIsCorruptMito.3BadContainers.false.bug8768.tsv",
},

// cloud file test
{
// 0 bad containers
"gs://hellbender/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram",
"gs://hellbender/test/resources/large/human_g1k_v37.20.21.fasta",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.cloud.txt",
}
// 0 bad containers
"gs://hellbender/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram",
"gs://hellbender/test/resources/large/human_g1k_v37.20.21.fasta",
List.of(Pair.of(CRAMIssue8768Detector.VERBOSE_ARG_NAME, "false")),
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.cloud.txt",
"src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.cloud.tsv",
},
};
}

@Test(dataProvider = "cramAnalysisTestCases")
@Test(dataProvider = "cramAnalysisTestCases", groups={"cloud"})
public void testCramAnalysis(
final String inputPath,
final String referencePath, // unused for now
final List<Pair<String, String>> extraArgs,
final String expectedOutputPath) throws IOException {
final File outFile = createTempFile("testFileDiagnostics", ".txt");
final String expectedTextOutputPath,
final String expectedTSVOutputPath) throws IOException {
final File outTextFile = createTempFile("testFileDiagnostics", ".txt");
final File outTSVFile = expectedTSVOutputPath == null ? null : createTempFile("testFileDiagnostics", ".tsv");
ArgumentsBuilder argBuilder = new ArgumentsBuilder();
argBuilder.addInput(inputPath);
argBuilder.addOutput(outFile);
argBuilder.addOutput(outTextFile);
argBuilder.addReference(Paths.get(referencePath));
if (outTSVFile != null) {
argBuilder.add(CRAMIssue8768Detector.OUTPUT_TSV__ARG_NAME, outTSVFile.getAbsolutePath());
}
if (extraArgs != null) {
extraArgs.forEach(argPair -> argBuilder.add(argPair.getKey(), argPair.getValue()));
}
runCommandLine(argBuilder.getArgsList());

IntegrationTestSpec.assertEqualTextFiles(outFile, new File(expectedOutputPath));
IntegrationTestSpec.assertEqualTextFiles(outTextFile, new File(expectedTextOutputPath));
if (outTSVFile != null) {
IntegrationTestSpec.assertEqualTextFiles(outTSVFile, new File(expectedTSVOutputPath));
}
}

}

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