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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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SamLocusAndReferenceIterator fails with leading indels at the start of the reference #1481

Closed nh13 closed 4 years ago

nh13 commented 4 years ago

This comes from https://github.com/broadinstitute/picard/issues/1511

nh13 commented 4 years ago

@yfarjoun I haven't contributed in a while, but could you take a look, or assign someone who can?

codecov-commenter commented 4 years ago

Codecov Report

Merging #1481 into master will increase coverage by 0.013%. The diff coverage is 100.000%.

@@               Coverage Diff               @@
##              master     #1481       +/-   ##
===============================================
+ Coverage     69.203%   69.216%   +0.013%     
- Complexity      8701      8704        +3     
===============================================
  Files            588       588               
  Lines          34581     34583        +2     
  Branches        5779      5780        +1     
===============================================
+ Hits           23931     23937        +6     
+ Misses          8368      8366        -2     
+ Partials        2282      2280        -2
Impacted Files Coverage Δ Complexity Δ
...mtools/reference/SamLocusAndReferenceIterator.java 100.000% <100.000%> (ø) 5.000 <0.000> (+1.000)
...va/htsjdk/samtools/util/AbstractLocusIterator.java 70.950% <0.000%> (+0.559%) 66.000% <0.000%> (+1.000%)
...samtools/util/AsyncBlockCompressedInputStream.java 76.000% <0.000%> (+4.000%) 13.000% <0.000%> (+1.000%)
nh13 commented 4 years ago

@lbergelson can you make a release with this so I can update Picard?

lbergelson commented 4 years ago

@nh13 Yes. I want to do one very soon for other reasons as well. Can you wait a few days until I get a few other things merged?

nh13 commented 4 years ago

Excellent, a couple days would be great!!!

nh13 commented 4 years ago

@lbergelson welcome back from holiday, do you think you'll be able to get to it this week? I see the last release 2.21.3 was Mar 9, so there may well be a good set of other changes to include too.

lbergelson commented 4 years ago

Thanks. My hope is to get it out in the next day or two.

lbergelson commented 4 years ago

There are some changes in the pipe that people also want out but probably won't get merged by then so we'll probably do another one pretty quickly.

lbergelson commented 4 years ago

@nh13 2.22.0 is released and should be available in central soon