Source: samtools Version: 1.16.1-1 Severity: important Tags: ftbfs Hi,
When samtools is tested against htslib 1.17 now available in
experimental, I witness the following error, either from build
time checks or from autopkgtest:
The command failed [256]:
/tmp/autopkgtest.PsRbbX/autopkgtest_tmp/samtools view -e 'pos<1000||pos>1200'
-O cram,embed_ref=1 -T test/dat/mpileup.ref.fa -o
/tmp/autopkgtest.PsRbbX/autopkgtest_tmp/test/reference/mpileup.1.tmp.cram
test/dat/mpileup.1.sam
out:
err:[E::validate_md5] SQ header M5 tag discrepancy for reference '17'
[E::validate_md5] Please use the correct reference, or consider using
embed_ref=2
samtools view: error closing
"/tmp/autopkgtest.PsRbbX/autopkgtest_tmp/test/reference/mpileup.1.tmp.cram": -1
at ./test/test.pl line 98.
main::error("The command failed [256]:
/tmp/autopkgtest.PsRbbX/autopkgtest"..., "out:\x{a}", "err:[E::validate_md5] SQ
header M5 tag discrepancy for refere"...) called at ./test/test.pl line 211
main::cmd("/tmp/autopkgtest.PsRbbX/autopkgtest_tmp/samtools
view -e 'pos"...) called at ./test/test.pl line 3284
main::test_reference(HASH(0x55783ebcc4b8)) called at
./test/test.pl line 37
The issue doesn't occur against htslib 1.16 in unstable. The
good news is: this is the only issue I caught so far by bumping
the htslib version, so I'm pretty confident there were no major
breakages in the maneuver (think ABI, although the introduction
of versioned symbols upstream did involve a rather dense diff in
the symbols file). The fix might be as easy as bumping samtools
to version 1.17 too. Mostly documenting it via the bug tracker
since experimental pseudo-migrations are not back online yet.
Have a nice day, :)
Étienne.
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