Allow --reference-file to use compressed BGZIP files

[edsu7]

As per Linda's comment in #229 (comment):

The following doesn't work:

score-client view --object-id 1bd03148-7c5e-5a03-8271-a931ed2ab5ea --query chr1:10000-20000 --reference-file /reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa.gz

But the uncompressed version does:

score-client view --object-id 1bd03148-7c5e-5a03-8271-a931ed2ab5ea --query chr1:1000-20000 --reference-file /reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa

We suspect this is due to the 2.1.0 version of HTSJDK library.
https://github.com/samtools/htsjdk/releases/tag/2.16.0 makes mention of supporting compressed files.

Updating HTSJDK may resolve the issue

[edsu7]

Found this dependabot issue as well, so we may have a branch underway just needs testing and merging
overture-stack/score#342

[dahiyaAD]

Link to PR - overture-stack/score#363

[edsu7]

Ran the following test - Fix looks great
Setup cmd:

docker run -d -it --name prod-score-client -e ACCESSTOKEN=${token}-e STORAGE_URL=https://api.platform.icgc-argo.org/storage-api -e METADATA_URL=https://api.platform.icgc-argo.org/storage-api --mount type=bind,source=/home/ubuntu/downloads/example_sarek/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/,target=/references overture/score:75ca0a3

Compress cmd:

docker exec prod-score-client sh -c "score-client view --object-id 1bd03148-7c5e-5a03-8271-a931ed2ab5ea --query chr1:1000-20000 --reference-file /references/Homo_sapiens_assembly38.fasta.gz" | wc -l

Uncompressed:

docker exec prod-score-client sh -c "score-client view --object-id 1bd03148-7c5e-5a03-8271-a931ed2ab5ea --query chr1:1000-20000 --reference-file /references/Homo_sapiens_assembly38.fasta" | wc -l

Both had the same output:

Running...Viewing...                                                            
Validating repository connection...
5782 

One minor issue was that since the upgrade the execution time has gone from:

real	0m32.943s
user	0m0.038s
sys	0m0.168s

to

real	4m58.370s
user	0m0.065s
sys	0m0.179s

cmd:

time docker exec prod-score-client sh -c "score-client view --object-id 1bd03148-7c5e-5a03-8271-a931ed2ab5ea --query chr1:1000-20000 --reference-file /references/Homo_sapiens_assembly38.fasta"

[lindaxiang]

Tested with overture/score:75ca0a3, and have the same observation as what Edmund has documented above.
Other than execution time becomes very long, no other major issues are found.