JACUSA2 pileup for one sample

[dingtiany]

Hi! piechottam,
I'm sorry to bother you.
And when try use one bam file to SNV detect,
the code:'java -jar ~/software/jacusa/JACUSA_v2.0.4.jar pileup -r test_file -R cleaned.fa -p 6 -s sample.bam'
it come some error like:'INFO 00:00:01 Thread 3: Working on contig 1:800028-900027
java.lang.NullPointerException: Cannot invoke "lib.data.DataContainer.getUnstrandedRefBase()" because "provider" is null
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)'
but when I use >1 sample bam files, there is not error any more.
What can I do to solve this?
Thanks for your help.
Best.

[piechottam]

This seems to be a bug. Currently, i am on vaccation and i will look into this next week.

Quick fix
If you are interesed in the pileup, use sample.bam twice and remove the bases21 column.