use IntelDeflaterFactory from the GKL #1964
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| @@ -128,6 +129,13 @@ public Object instanceMainPostParseArgs() { | |||
| System.setProperty("java.io.tmpdir", f.getAbsolutePath()); // in loop so that last one takes effect | |||
| } | |||
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| //Set defaults (note: setting them here means they are not controllable by the user) | |||
| BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory()); | |||
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Add a command-line arg to CommandLineProgram that allows the user to opt-out of using the IntelDeflater
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i'll grab it |
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note: This PR does not reinstate the IntelDeflater for Spark. It's now a bit tricky because you need to call |
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GKL 0.1.1 release in Maven Central resolves IntelLabs/GKL#8 (not the Spark issue) |
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thanks @gspowley - using 0.1.1 now and the issue is fixed |
This was referenced Jul 1, 2016
This was referenced Jul 5, 2016
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fixes #1903
also updated the system properties in build.gradle and gatk-launch