Bug#1139484: picard-tools: FTBFS: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference

[Pierre Gruet]

Hi Andreas,


Le 30/06/2026 à 15:53, Andreas Tille a écrit :

Hi Pierre and others,

it seems the problem occures when creating the docs.  I wonder whether
there is some simple solution for this problem or whether it might be a
sensible means to deal with this problem by just not generating the docs
and remove the libpicard-java-doc package.

I understand better, I pulled your changes and got problems with the doc. B-D again on default-jdk instead of default-jdk-headless fixes this, although we can really have a discussion about dropping the -doc package nonetheless. I get the 4 failing tests of the bug report again, I feel there is an issue in a class of htsjdk, which has undergone changes in the last few days as I can see in the upstream repository. I suggest to wait for the next upstream release of htsjdk as it should fix the issue, hopefully.

Kind regards
     Andreas.

All the best,

--
Pierre

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