Chris Norman
Chris Norman
I re-enabled the code in `Block` that rejects contentID=0 for external, and validated the every test failure is due to one of the files above. So although we should regenerate...
@AlexanderSenf Thanks for the update on this. We are making some progress on being able to upgrade to Java 11, but we're not quite there yet. Any idea how this...
@bioinfornatics Oh - can you run `od -c -N 30 ` and include the results here. You may be hitting this embarrassing bug which we've never fixed https://github.com/samtools/htsjdk/issues/946.
Yes, that looks like a gzip header. Sadly, htsjdk lacks support for gzipped BCF, as mentioned above.
Someone else may have a more definitive answer, but I think the linear index part of a Tribble index (.idx) has that information, per-chromosome. I don't think tabix does.
I think the likelihood of issues is low, but its probably worth at least profiling to see if inlining helps. The main issue is that the variable being tested isn't...
Related to: https://github.com/samtools/htsjdk/issues/628.
@lindenb There is a PR that has a pretty big [refactoring](https://github.com/samtools/htsjdk/pull/835) of the header line hierarchy in an attempt to fix a number of issues similar to this one. (One...
BTW, I'd be curious to know more about which GATK version and tool/code path failed. There are tests in both Picard and GATK where this exact case occurs (a set...
@lindenb Yeah, I've seen this issue with SelectVariants in both GATK3 and 4. Thanks.