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

Thu, 02 Jul 2026 12:05:20 -0700 

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 have also looked at this bug, on my machine I can see there are four failing tests (which seems to be consistent with the title of the bug report), I have not reached the build of the documentation yet.
So far I have not found what is going wrong in the tests. Some weeks ago I updated htsjdk to version 5.0.0, this might be the reaso although I don't remember picard FTBFS'ed at that time :/ Let's continue to investigate... 



Kind regards
     Andreas.



All the best,

--
Pierre

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