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Upgrade htsjdk to v3.0.0. #7867

Merged
merged 6 commits into from
Jul 18, 2022
Merged

Upgrade htsjdk to v3.0.0. #7867

merged 6 commits into from
Jul 18, 2022

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cmnbroad
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gatk-bot commented May 24, 2022 •
edited

Github actions tests reported job failures from actions build 2378038203
Failures in the following jobs:

Test Type JDK Job ID Logs
unit 11 2378038203.13 logs
integration 11 2378038203.12 logs
unit 8 2378038203.1 logs
integration 8 2378038203.0 logs

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codecov bot commented May 24, 2022 •
edited

Codecov Report

Merging #7867 (aa45aa8) into master (804d1e2) will increase coverage by 0.011%.
The diff coverage is 80.000%.

@@               Coverage Diff               @@
##              master     #7867       +/-   ##
===============================================
+ Coverage     87.078%   87.089%   +0.011%     
+ Complexity     36997     36993        -4     
===============================================
  Files           2217      2217               
  Lines         173849    173847        -2     
  Branches       18791     18791               
===============================================
+ Hits          151385    151402       +17     
+ Misses         15832     15818       -14     
+ Partials        6632      6627        -5
Impacted Files Coverage Δ
...bender/tools/funcotator/StrandCorrectedAllele.java 0.000% <ø> (ø)
...nstitute/hellbender/utils/haplotype/Haplotype.java 90.244% <ø> (ø)
...kers/haplotypecaller/AssemblyBasedCallerUtils.java 90.517% <66.667%> (-0.041%) ⬇️
...itute/hellbender/engine/spark/GATKRegistrator.java 100.000% <100.000%> (ø)
...lbender/tools/sv/cluster/CanonicalSVCollapser.java 87.471% <0.000%> (-0.464%) ⬇️
...itute/hellbender/tools/LocalAssemblerUnitTest.java 92.448% <0.000%> (ø)
.../hellbender/utils/genotyper/AlleleLikelihoods.java 90.349% <0.000%> (+0.205%) ⬆️
...lbender/utils/variant/GATKVariantContextUtils.java 87.224% <0.000%> (+0.232%) ⬆️
...llbender/tools/spark/sv/evidence/ReadMetadata.java 88.480% <0.000%> (+0.245%) ⬆️
...er/tools/spark/sv/evidence/BreakpointEvidence.java 79.206% <0.000%> (+0.467%) ⬆️
... and 12 more

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Github actions tests reported job failures from actions build 2378939111
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 2378939111.10 logs

@cmnbroad cmnbroad force-pushed the cn_update_htsjdk branch 2 times, most recently from 9422664 to c8aca92 Compare June 7, 2022 12:18
@cmnbroad cmnbroad changed the title DRAFT: Changes for htsjdk update. Upgrade htsjdk to v3.0.0. Jun 7, 2022
@cmnbroad cmnbroad marked this pull request as ready for review June 7, 2022 12:23
@cmnbroad cmnbroad marked this pull request as draft June 7, 2022 12:25
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cmnbroad commented Jun 7, 2022 •
edited

Draft until we have a Picard release with broadinstitute/picard#1812.

@cmnbroad cmnbroad force-pushed the cn_update_htsjdk branch 3 times, most recently from 08906d4 to 14b8624 Compare June 13, 2022 21:56
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droazen commented Jun 14, 2022

@cmnbroad Is this one ready for review?

@cmnbroad cmnbroad marked this pull request as ready for review June 14, 2022 16:19
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@droazen Yeah, I had just forgotten to take it out of draft after the Picard update.

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droazen approved these changes Jun 14, 2022
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👍 Merge when ready @cmnbroad

@cmnbroad cmnbroad merged commit ace7821 into master Jul 18, 2022
@cmnbroad cmnbroad deleted the cn_update_htsjdk branch July 18, 2022 20:34
jamesemery added a commit that referenced this pull request Jul 21, 2022
@jamesemery
Revert "Upgrade htsjdk to v3.0.0. (#7867)"
ec9d1b6 
This reverts commit ace7821. This is a necessary step in order for #7876 to be merged
jamesemery added a commit that referenced this pull request Jul 22, 2022
@jamesemery
Revert "Upgrade htsjdk to v3.0.0. (#7867)" (#7960)
5f9f12b 
This reverts commit ace7821. This is a necessary step in order for #7876 to be merged
lbergelson added a commit that referenced this pull request Sep 19, 2022
@lbergelson
Revert "Revert "Upgrade htsjdk to v3.0.0. (#7867)" (#7960)"
77faccb 
This reverts commit 5f9f12b.
lbergelson added a commit that referenced this pull request Sep 19, 2022
@lbergelson
Upgrade htsjdk to v3.0.0.
5b89e89 
This upgrades htsjdk to v3.0.0 which was attempted in #7867 and then reverted in #7960
in order to unblock the jukebox merge.
@lbergelson lbergelson mentioned this pull request Sep 19, 2022
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lbergelson added a commit that referenced this pull request Oct 12, 2022
@lbergelson
Upgrade htsjdk to v3.0.0.
d8b0882 
This upgrades htsjdk to v3.0.0 which was attempted in #7867 and then reverted in #7960
in order to unblock the jukebox merge.
lbergelson added a commit that referenced this pull request Oct 12, 2022
@lbergelson @droazen
Upgrade htsjdk to v3.0.1 and picard to 2.27.5 (#8025)
8dbb78f 
This upgrades htsjdk h was attempted in #7867 and then reverted in #7960
in order to unblock the jukebox merge.

* upgrade htsjdk 2.24.1 -> 3.0.1
* upgrade picard 2.27.1 -> 2.27.5

Co-authored-by: David Roazen <[email protected]>
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