Bump htsjdk to 3.0.3 #884
Bump htsjdk to 3.0.3 #884
Conversation
| }.head | ||
| // TODO: could use a TreeSet to store the iterators, examine the head of each iterator, then pop the iterator with the min, | ||
| // and add that iterator back in. | ||
| iterators.zipWithIndex.map { case(iter, idx) => | ||
| if (iter.isEmpty || this.comparator.compare(minCtx, iter.head) != 0) None | ||
| iterators.map { iter => |
There was a problem hiding this comment.
The variable idx wasn't used and zipWithIndex is slower than mapping.
|
|
||
| if (iters.isEmpty) throw new IllegalArgumentException("No iterators given") | ||
|
|
||
| private val iterators = iters.map(_.buffered) | ||
| private val comparator = dictOrComp match { | ||
| case Left(dict) => new VariantContextComparator(dict.asSam) |
There was a problem hiding this comment.
The class VariantContextComparator now compares more than just on location (source)
Searching the codebase, this was the only improper use of the new class (and unit tests were failing).
Codecov ReportBase: 95.66% // Head: 95.66% // No change to project coverage 👍
Additional details and impacted files@@ Coverage Diff @@
## main #884 +/- ##
=======================================
Coverage 95.66% 95.66%
=======================================
Files 125 125
Lines 7239 7239
Branches 507 495 -12
=======================================
Hits 6925 6925
Misses 314 314
Flags with carried forward coverage won't be shown. Click here to find out more.
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
|
Dropping to draft as there is still an entrypoint for |
| } | ||
|
|
||
| @deprecated("VariantContextComparator will no longer compare variant contexts on location alone.") | ||
| def apply(iters: Seq[Iterator[VariantContext]], |
There was a problem hiding this comment.
This entrypoint was never used in this codebase. And it is no longer possible to use VariantContextComparator since it compares variants beyond location alone (source). Seems like my only option is deprecation and raising an exception.
|
@tfenne there is a breaking change in this PR so I assigned you too. |
|
Closing as htsjdk reverted the changes that were in this point release. |
Changelog for htsjdk is here (using non-snapshot root): samtools/htsjdk@2.24.1...3.0.3