picard-tools progress status

[Olivier Sallou <olivier.sallou@irisa.fr>]

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