Hi,
after quick and dirty packaging of picard new dependencies (done
locally, can't be uploaded in this state), I could build picard-tools.
However, there are many failing tests (168 at this time), though ~2800
tests are fine.
Some failures I can"t explain (freezing, thread errors , with no
detailled log) and others where picard seems to fail with htsjdk (the
one from experimental, with nio errors).
I am not really confident that I will be able to debug all those errors,
which may be related to debian env (patching, gradle etc...) or from
packaged dependencies.
For htsjdk test errors, it seems they are all related with 2 recurrent
errors among failed tests
htsjdk.samtools.SAMException: Error parsing interval list.
at htsjdk.samtools.util.IntervalList.fromReader(IntervalList.java:512)
at htsjdk.samtools.util.IntervalList.fromPath(IntervalList.java:409)
at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:399)
at
picard.util.IntervalListTools$IntervalListInputType$2.getIntervalListInternal(IntervalListTools.java:494)
htsjdk.samtools.util.RuntimeIOException:
java.nio.channels.ClosedByInterruptException
at
htsjdk.samtools.util.BufferedLineReader.readLine(BufferedLineReader.java:70)
at htsjdk.samtools.liftover.Chain.loadChain(Chain.java:334)
at htsjdk.samtools.liftover.Chain.loadChains(Chain.java:318)
at htsjdk.samtools.liftover.LiftOver.<init>(LiftOver.java:89)
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:263
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
