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Merge discvr 20.3 #45

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Merged
bbimber merged 39 commits into from
Jul 10, 2020
Merged

Merge discvr 20.3 #45

bbimber merged 39 commits into from
Jul 10, 2020

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@bbimber
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@bbimber bbimber commented Jul 10, 2020

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bbimber added 30 commits May 26, 2020 21:22
@bbimber
Mark intermediate BAMs for deletion in pipeline
4854557
@bbimber
Migrate DepthOfCoverage to GARK4
e0866a8
@bbimber
Report depth by amplicon
ef66ee8
@bbimber
Pass -L to DepthOfCoverage in all cases
a228277
@bbimber
Retain TSV output for DepthOfCoverage
7da56ad
@bbimber
Delete output BAM if it exists for lofreq indelqual
c2835be
@bbimber
Use annotated VCF as output
112dbd7
@bbimber
Don't use thousands separator in table output
d986d08
@bbimber
Also report median depth over amplicons
4cd3f96
@bbimber
After failure, ensure we delete the working copy of the GenomicsDB wo…
d81e274 
…rkspace and remake.
@bbimber
Add additional feature attributes to index
bc63b67
@bbimber
Support MINIMUM_DISTANCE for MarkDuplicatesWithMate
b211262
@bbimber
Fault tolerance for ApplyBQSR
1642168
@bbimber
Ensure wait indicator hidden
511eccc
@bbimber
Add check to prevent STAR submission without GTF unless specifically …
4e17954 
…chosen
@bbimber
Bugfix GenomicsDBImport
a965517
@bbimber
Allow GenomicsDBWorkspace as input
9b62372
@bbimber
Create FileType for GenomicsDB
0b26061
@bbimber
Bugfix STAR validation
6eddc8f
@bbimber
Add --genomicsdb-use-vcf-codec workaround to GenotypeGVCFs
9563a46
@bbimber
ChangeReadsetStatus broken from earlier refactor
059f50c
@bbimber
Switch svn -> github
8c0fcec
@bbimber
upgrade to dijit 1.6.3 based on dependabot recommendation
a3939c1
@bbimber
capture mean coverage as metric for lofreq
e5072b5
@bbimber
Favor DataRegion getChecked over getSelected
987fa29
@bbimber
Add more logging
94bed15
@bbimber
Improve log message
6ed20c7
@bbimber
Allow TagPcrSummary to run without designing primers
fdd45a4
@bbimber
Do not add outputs that will not be created
fc786b9
@bbimber
Do not add sequence outputs that will not be created
303c8fb
@labkey-jeckels labkey-jeckels changed the base branch from release20.7 to release20.7-SNAPSHOT July 10, 2020 21:57
@bbimber bbimber merged commit 72d94ba into release20.7-SNAPSHOT Jul 10, 2020
@bbimber bbimber deleted the fb_merge_discvr-20.3 branch July 10, 2020 22:10
bbimber pushed a commit that referenced this pull request Jun 26, 2021
@jctrotter
Removed unused commented code block (#45)
96ec106
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@labkey-jeckels labkey-jeckels labkey-jeckels approved these changes

@labkey-tchad labkey-tchad Awaiting requested review from labkey-tchad

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3 participants

@bbimber @labkey-jeckels