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blachlylab / dhtslib

D bindings and OOP wrappers for htslib
MIT License
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Update htslib bindings to Htslib 1.16 #136

Closed charlesgregory closed 2 years ago

jblachly commented 2 years ago

Comments:

  1. Thank goodness for Dstep and automated conversion
  2. This is way too much to review by hand, so probably just go ahead and merge it
  3. I saw there is new base modification features, any other cool new features?

I saw that the accompanying samtools release -- don't know if it requires new features in htslib or not -- adds template coordinate sorting . That is huge because it can bypass a couple of steps required for deduping (don't have to apply custom tag, then group by tag , sort by coord, etc)

jblachly commented 2 years ago

Incidentally, all the tests failed, so probably don't merge yet.

charlesgregory commented 2 years ago

I saw that the accompanying samtools release -- don't know if it requires new features in htslib or not -- adds template coordinate sorting . That is huge because it can bypass a couple of steps required for deduping (don't have to apply custom tag, then group by tag , sort by coord, etc)

I just saw the base modification stuff and some more cram stuff exposed so.

I will get the tests fixed. I'll make a merge to master and a new release.

codecov[bot] commented 2 years ago

Codecov Report

Merging #136 (8352fdb) into develop (e79880f) will decrease coverage by 2.51%. The diff coverage is 10.19%.

@@             Coverage Diff             @@
##           develop     #136      +/-   ##
===========================================
- Coverage    85.88%   83.37%   -2.52%     
===========================================
  Files           45       45              
  Lines         4682     4823     +141     
===========================================
  Hits          4021     4021              
- Misses         661      802     +141
Impacted Files Coverage Δ
source/dhtslib/memory.d 73.07% <ø> (ø)
source/htslib/bgzf.d 100.00% <ø> (ø)
source/htslib/cram.d 0.00% <ø> (ø)
source/htslib/hfile.d 26.66% <ø> (ø)
source/htslib/hts.d 0.00% <ø> (ø)
source/htslib/kstring.d 60.41% <ø> (ø)
source/htslib/sam.d 7.92% <0.00%> (-48.60%) :arrow_down:
source/htslib/vcf.d 14.89% <ø> (ø)
source/dhtslib/file/iterator.d 96.33% <100.00%> (ø)
source/dhtslib/vcf/reader.d 94.25% <100.00%> (ø)
... and 2 more

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