Update imports to htslib/samtools/bcftools 1.17 #1172
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For each package:
rm -rf htslib; python3 devtools/import.py htslib .../htslib-1.17
rm -rf samtools; python3 devtools/import.py samtools .../samtools-1.17
rm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.17
Take care to preserve the #define additions to bcftools/regidx.h.
(Don't bother adding {sam,bcf}tools/htslib-1.17/{LICENSE,**/README}.)
Spell the former as `pysam.samtools.cram_size` so it is a valid identifier.
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Great, thanks! |
AndreasHeger
approved these changes
Mar 15, 2023
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This one was pretty straightforward: just the imports themselves, and two new samtools subcommands to add.
(Re the upcoming release… There's a few minor bug fixes to other things that I still want to commit, and a couple of more major Python 3.11 or macOS M1 things still in flight, notably #1146, #1149, and #1151.)