Test out the preview version of the next GKL (DO NOT MERGE)

[droazen]

Test out the preview version of the GKL, containing the new native PDHMM.

The jar was build using Java 1.8 and contains AVX optimized binaries for Linux hosts and not optimized binaries for Mac (Intel CPUs)

Example code showing how to call into the PDHMM is here:
https://github.com/Intel-HLS/GKL/blob/master/src/test/java/com/intel/gkl/pdhmm/IntelPDHMMUnitTest.java

[droazen]

@jamesemery Here's the branch we discussed -- see my notes above.

[jamesemery]

A command line that triggered the crash in our testing:

gatk HaplotypeCaller -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta -I gs://broad-dsde-methods-dragen/reprocessed_data_v3.7.5_masked/CH1_CHM13_WGS1/CH1_CHM13_WGS1.bam -L /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/109scattered.interval_list -O CH1_CHM13_WGS1.vcf.gz --pileup-detection --pileup-detection-absolute-alt-depth 0 --pileup-detection-bad-read-tolerance 0.4 --pileup-detection-enable-indel-pileup-calling --pileup-detection-active-region-phred-threshold 3.0 --use-pdhmm -contamination 0.0 -G StandardAnnotation -G StandardHCAnnotation --dragen-mode --disable-spanning-event-genotyping --dragstr-params-path /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-DragstrAutoCalibration/CH1_CHM13_WGS1.bam.dragstr -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90

--dragstr-params-path /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-DragstrAutoCalibration/CH1_CHM13_WGS1.bam.dragstr is likely optional

-L is optional and any interval will likely work to reproduce the error.