Update imports to htslib/samtools/bcftools 1.21 #1310
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Fix import prevention for HTSlib utilities and prevent importing
the new htslib/annot-tsv.c utility and the hts_probe_cc.sh script.
Also import config.{guess,sub} for HTSlib, required now that configure
has been generated with autoconf 2.72.
In samtools/bamtk.c, remove `fclose(stdout)` as the pysam wrapper will
reuse this file handle.
In v1.21+ HTSlib's CRAM implementation rejects mapped reads at pos -1. Make the test case's read unmapped to avoid this, and tidy up the tmpfile handling (which was commented out previously in some checked-in tmp code).
For each package:
rm -rf htslib; python3 devtools/import.py htslib .../htslib-1.21
rm -rf samtools; python3 devtools/import.py samtools .../samtools-1.21
rm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.21
Take care to preserve the #define additions to bcftools/regidx.h.
(Don't bother adding {sam,bcf}tools/htslib-1.21/{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 1.21. Significant additional considerations:
In samtools/bamtk.c, remove
fclose(stdout)as the pysam wrapper will reuse this file handle. The tests will fail on Linux if this stdout-closing is left in.Also import config.{guess,sub} for HTSlib, required now that configure has been generated with autoconf 2.72. And add them to MANIFEST.in.
Continue to take care to preserve removing the regeneration of htscodecs.mk from htslib/Makefile.
Fix
TestHeaderWriteReadtest case: In v1.21+ HTSlib's CRAM implementation rejects mapped reads at pos -1.