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samtools / htslib-plugins

Plugins for use with HTSlib
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Plugin issue with iRODS >4.3.0 #6

Open kjsanger opened 1 year ago

kjsanger commented 1 year ago

samtools 1.18 htslib-plugins: 201712

Running the following (which is from one of our test suites which passes on iRODS 4.2.7, 4.2.11 and 4.2.12) fails in iRODS >4.3.0

samtools view -C -T ./t/data/aln_data_object/test_ref.fa -o irods:/testZone/home/irods/Illumina::AlnDataObjectTest.53621.19/7915_5\#0.cram ./t/data/aln_data_object/7915_5\#0.sam

We see:

'samtools: /opt/irods-externals/boost1.81.0-0/include/boost/smart_ptr/shared_ptr.hpp:783: typename boost::detail::sp_member_access<T>::type boost::shared_ptr<irods::network>::operator->() const [T = irods::network]: Assertion `px != 0' failed.'

The client and server are both >4.3.0, built from the 4-3-stable iRODS branch. We have Docker containers of the client/server combo exhibiting the issue, should anyone want to reproduce this:

ghcr.io/wtsi-npg/ub-22.04-irods-4.3-nightly:4.3 ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3-nightly:4.3

These contain unofficial Debian package builds created with RENCI's iRODS development environment which we're using to get ahead of potential issues with future iRODS releases, before they impact us.

Thanks.