Update to GKL version 0.8.8

[droazen]

No description provided.

[droazen]

@lbergelson please review

[gatk-bot]

Travis reported job failures from build 33752
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	openjdk11	33752.14	logs
cloud	openjdk8	33752.1	logs
unit	openjdk11	33752.13	logs
integration	openjdk11	33752.12	logs
variantcalling	openjdk8	33752.4	logs
unit	openjdk8	33752.3	logs
conda	openjdk8	33752.5	logs
integration	openjdk8	33752.2	logs
cloud	openjdk11	33752.14	logs
cloud	openjdk8	33752.1	logs
unit	openjdk11	33752.13	logs
integration	openjdk11	33752.12	logs
variantcalling	openjdk8	33752.4	logs
conda	openjdk8	33752.5	logs

[lbergelson]

Oh man. They beat me to it.

[lbergelson]

👍

[droazen]

Seeing some test failures unfortunately due to the following error:

java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.fs.FileSystem
        at org.apache.hadoop.fs.Path.getFileSystem(Path.java:365)

[gatk-bot]

Travis reported job failures from build 33778
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	openjdk8	33778.1	logs
cloud	openjdk11	33778.14	logs
unit	openjdk11	33778.13	logs
integration	openjdk11	33778.12	logs
variantcalling	openjdk8	33778.4	logs
unit	openjdk8	33778.3	logs

[droazen]

Added a commit to remove the FPGA PairHMM implementation as an option from GATK, since it's been removed from the GKL.

[gatk-bot]

Travis reported job failures from build 34034
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	openjdk8	34034.1	logs
cloud	openjdk11	34034.14	logs
unit	openjdk11	34034.13	logs
integration	openjdk11	34034.12	logs
variantcalling	openjdk8	34034.4	logs
conda	openjdk8	34034.5	logs
unit	openjdk8	34034.3	logs
integration	openjdk8	34034.2	logs

[lbergelson]

@droazen I believe I've found the problem here and pushed a fix.

[lbergelson]

We'll see if tests pass.

[droazen]

Thank you @lbergelson for the fix! For once a dependency conflict that turns out to be simple!