Tool to detect CRAM base corruption caused by GATK issue 8768 #8819
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Github actions tests reported job failures from actions build 8992751464
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Github actions tests reported job failures from actions build 9063387853
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Github actions tests reported job failures from actions build 9065623255
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| * A diagnostic tool that analyzes a CRAM input file to look for conditions that trigger issue 8768. | ||
| * | ||
| * Writes a report to a file indicating whether the file appears to have read base corruption caused by 8768. | ||
| * |
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Add a 1-2 paragraph description of the bug here, including under what circumstances it gets triggered, how it manifests, and what versions of GATK/Picard it affects. We should also post this information in a comment to issue 8768.
| @ExperimentalFeature | ||
| @WorkflowProperties | ||
| @CommandLineProgramProperties( | ||
| summary = "Analyze a CRAM file for issue 8768", |
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"Analyze a CRAM file to check for base corruption caused by issue 8768"
| @WorkflowProperties | ||
| @CommandLineProgramProperties( | ||
| summary = "Analyze a CRAM file for issue 8768", | ||
| oneLineSummary = "Analyze a CRAM file for issue 8768", |
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"Analyze a CRAM file to check for base corruption caused by issue 8768"
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| @Argument(fullName = StandardArgumentDefinitions.INPUT_LONG_NAME, | ||
| shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME, | ||
| doc = "Input path of file to analyze", |
| System.out.println(String.format("\nOutput written to %s\n", outputFile)); | ||
| BAMIndexer.createAndWriteIndex(inputPath.toPath().toFile(), outputFile, true); | ||
| System.out.println(String.format("\nOutput written to %s\n", outputPath)); | ||
| // note this method is not nio aware |
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Should probably note this limitation in the class-level docs as well
| @@ -0,0 +1,126 @@ | |||
| package org.broadinstitute.hellbender; | |||
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This test should be in the tools package
| @@ -81,6 +81,7 @@ public void testFileToFile(String fileIn, String extOut, String reference) throw | |||
| @DataProvider(name="testingData") | |||
| public Object[][] testingData() { | |||
| return new String[][]{ | |||
| // {"/Users/cnorman/projects/gatk/ultMerge.testfix.cram", ".cram", "/Users/cnorman/projects/gatk/Homo_sapiens_assembly19_1000genomes_decoy.fasta"}, | |||
droazen
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