Fix #117 corollary - if QUAL is . set to 0

[dnil]

This PR adds | fixes:

• Sentieon TNscope may set QUAL to . in addition to not outputting GQ for variants. Solve by setting gq 0 for these.

How to prepare for test:

• ssh to ...
• Install on stage:
  bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]

How to test:

• load case with . in QUAL (e.g. selectbison)

Expected outcome:

• works with patch, not with master

Review:

• Code approved by HS, VI
• Tests executed by DN
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[henrikstranneheim]

👍

[ivadym]

Nice 💯 , thanks @dnil!

[dnil]

✅ Tested on loqusdb-stage.

❌ with 2.7.3:

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_loqusdb -t loqusdb -b 2.7.3
loqusdb-somatic load --case-id selectbison --variant-file SNV.somatic.selectbison.tnscope.clinical.filtered.pass.vcf.gz --sv-variants SV.somatic.selectbison.svdb.clinical.filtered.pass.vcf.gz --qual-gq

✅ with this branch:

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_loqusdb -t loqusdb -b qual_dot
loqusdb-somatic load --case-id selectbison --variant-file SNV.somatic.selectbison.tnscope.clinical.filtered.pass.vcf.gz --sv-variants SV.somatic.selectbison.svdb.clinical.filtered.pass.vcf.gz --qual-gq

[dnil]

Deployed to prod: