Update imports to htslib/samtools/bcftools 1.22 #1343
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Omit the htslib/ref_cache/ source code, and hard-code a configure --disable-ref-cache argument accordingly. BCFtools's mpileup2/* is currently used only by plugins/vrfs.c which we don't wrap, so we can (for now) omit this mpileup2/* code too.
For each package:
rm -rf htslib; python3 devtools/import.py htslib .../htslib-1.22
rm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22
rm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.22
Take care to preserve the #define additions to bcftools/regidx.h.
(Don't bother adding {sam,bcf}tools/htslib-1.22/{LICENSE,**/README}.)
Also take care to preserve removing the regeneration of htscodecs.mk
from htslib/Makefile.
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Import upstream htslib/samtools/bcftools 1.22. Significant additional considerations:
Omit the htslib/ref_cache/* code just as we omit htslib/bgzip.c et al. The configure script contains probes for the benefit of ref-cache and absolutely requires libcurl to be available, so we hard-code
--disable-ref-cachewhen invoking configure — as the source code is not present anyway.Continue to take care to preserve removing the regeneration of htscodecs.mk from htslib/Makefile.
The HTSlib 1.22 release contains significant operational changes — it emits CRAM 3.1 by default, and no longer consults EBI's reference server by default — so we will likely observe how the dust settles from those changes before merging this update.