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blachlylab / dhtslib

D bindings and OOP wrappers for htslib
MIT License
7 stars 1 forks source link

htslib 1.12 compatibility #79

Closed charlesgregory closed 3 years ago

charlesgregory commented 3 years ago

dstep was used to update bindings and add some previously unbound functions. Unittests are likely needed to ensure the functions are working correctly. One option could be to convert htslib's unit and integration tests into D unittests.

There are a lot of changes here. Mainly due to the fact that the generated bindings were added to the dstep folder along with their diffs along with being added to the htslib source folder.

hts_endian was converted by hand, it is probably not quite as performant but I intended to make it as close as possible which involved making custom structs for int8_t and int16_t due to issues with Dlang int promotion.

This pull request closes #35, #64, #78, and #72.

codecov-commenter commented 3 years ago

Codecov Report

Merging #79 (308ba43) into develop (5babdfa) will decrease coverage by 3.63%. The diff coverage is 8.33%.

:exclamation: Current head 308ba43 differs from pull request most recent head a61b033. Consider uploading reports for the commit a61b033 to get more accurate results Impacted file tree graph

@@             Coverage Diff             @@
##           develop      #79      +/-   ##
===========================================
- Coverage    72.16%   68.52%   -3.64%     
===========================================
  Files           22       27       +5     
  Lines         1872     1986     +114     
===========================================
+ Hits          1351     1361      +10     
- Misses         521      625     +104
Impacted Files Coverage Δ
source/dhtslib/vcf.d 75.07% <0.00%> (ø)
source/htslib/cram.d 0.00% <0.00%> (ø)
source/htslib/hts.d 0.00% <0.00%> (ø)
source/htslib/hts_log.d 100.00% <ø> (ø)
source/htslib/kbitset.d 0.00% <0.00%> (ø)
source/htslib/kroundup.d 0.00% <0.00%> (ø)
source/htslib/kstring.d 0.00% <ø> (ø)
source/htslib/sam.d 50.00% <ø> (ø)
source/htslib/tbx.d 0.00% <0.00%> (ø)
source/htslib/vcf.d 6.38% <ø> (ø)
... and 10 more

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jblachly commented 3 years ago

80 files changed, reviewing this is gonna be a "no" from me dog _meme.jpg.

I'll go ahead and merge this in, but I noticed on of your windows-specific functions was removed and made comment at the appropriate place