updating htsjdk to 2.18.1 #5486
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updating htjsdk 2.18.0 -> 2.18.1 this fixes an issue that prevents gatk from reading certain cram files
| @@ -57,7 +56,7 @@ repositories { | |||
| } | |||
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| final requiredJavaVersion = "8" | |||
| final htsjdkVersion = System.getProperty('htsjdk.version','2.18.0') | |||
| final htsjdkVersion = System.getProperty('htsjdk.version','2.18.1') | |||
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Can you add an integration test with one of the CRAMs in question that fails with 2.18.0 and passes with 2.18.1?
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Joel tried to build one and failed....
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I think he might have figured it out -- @jmthibault79 can you comment?
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Nope. samtools/htsjdk#1236
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I think it would be hard to generate one of these with htsjdk even if we had a fix for samtools/htsjdk#1236, since htsjdk doesn't use that (BetaEncoding) for alignment start; it uses ExternalIntegerEncoding. Its probably samtools that uses (or once used) that encoding for alignment start.
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Alright, fair enough -- we can merge this as-is then.
updating htjsdk 2.18.0 -> 2.18.1
this fixes an issue that prevents gatk from reading certain cram files