Upgrade htsjdk to v3.0.1 and picard to 2.27.5 #8025
Conversation
|
Github actions tests reported job failures from actions build 3084888525
|
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #8025 +/- ##
===============================================
- Coverage 86.643% 86.642% -0.001%
+ Complexity 38929 38927 -2
===============================================
Files 2334 2334
Lines 182616 182612 -4
Branches 20049 20048 -1
===============================================
- Hits 158224 158219 -5
+ Misses 17357 17356 -1
- Partials 7035 7037 +2
|
|
Github actions tests reported job failures from actions build 3085525827
|
droazen
changed the title
|
Github actions tests reported job failures from actions build 3229835669
|
lbergelson
force-pushed
the
lb_rerevert_htsjdk
branch
from
fd3f0a5
to
bdcb3c5
Compare
| private InverseAllele(final Allele allele, boolean isReference) { | ||
| super(allele, false); |
There was a problem hiding this comment.
i shudder to imagine where else we have made this mistake...
| public AlleleAndContext(final String contig, final int loc, final Allele allele, final Allele refAllele) { | ||
| super(allele, false); | ||
| super(allele.getBases(), allele.isReference()); |
There was a problem hiding this comment.
can we just get rid of all the old calls to this copy constructor.
There was a problem hiding this comment.
There are no other calls to it in our codebase, we can deprecate it and replace it with a more appropriately named method.
There was a problem hiding this comment.
can you also maybe depricate it because its confusing as hell and a trap?
This upgrades htsjdk to v3.0.0 which was attempted in #7867 and then reverted in #7960 in order to unblock the jukebox merge.