java issue with v2.0.1

[joegeorgeson]

Dear JACUSA2 team,

I am able to use v2.0.0-S-BETA-1 but v2.0.1 gives me the below error (using jre/8.121). Can you advise?

INFO   	00:00:00  Computing overlap between sequence records.
--------------------------------------------------------------------------------
JACUSA2 Version: 2.0.1 pileup -c 9 -q 20 -m 0 -P RF-FIRSTSTRAND -F 3844 -R hg19.fa -r out.jacusa in.bam
--------------------------------------------------------------------------------
INFO   	00:00:00  Thread 1: Working on contig chr1:10001-110000
java.lang.NullPointerException
	at lib.data.DefaultDataContainer.merge(DefaultDataContainer.java:180)
	at lib.data.DefaultDataContainer.merge(DefaultDataContainer.java:1)
	at lib.data.ParallelData.merge(ParallelData.java:134)
	at lib.data.ParallelData.getCombPooledData(ParallelData.java:80)
	at jacusa.method.rtarrest.CoverageStatistic.calculate(CoverageStatistic.java:21)
	at lib.stat.AbstractStat.filter(AbstractStat.java:16)
	at jacusa.worker.PileupWorker.process(PileupWorker.java:48)
	at lib.worker.AbstractWorker.doWork(AbstractWorker.java:139)
	at lib.worker.AbstractWorker.processReady(AbstractWorker.java:197)
	at lib.worker.AbstractWorker.run(AbstractWorker.java:213)

[piechottam]

Does the problem persist if you run?
... pileup -c 9 -q 20 -m 0 -P RF-FIRSTSTRAND -F 3844 -R hg19.fa -r out.jacusa in.bam in.bam

[joegeorgeson]

Does the problem persist if you run?
... pileup -c 9 -q 20 -m 0 -P RF-FIRSTSTRAND -F 3844 -R hg19.fa -r out.jacusa in.bam in.bam

That fixed it! I'm a bit confused, could I have found this in the documentation?

[piechottam]

You found a bug. JACUSA2 should work with only 1x (condition) "... in.bam". I'll fix it - thank you for your feedback!

[joegeorgeson]

Thank you very much for the help!!!