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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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complains about "the output is not to a file" with -r variable specified: #64

Open Izar-de-villasante opened 1 year ago

Izar-de-villasante commented 1 year ago

JACUSA2 Version: 2.0.1 call-2 -p 72 -filterNH 99 -filterNM 99 -c 3 -f=V -a E:file=dbsnp_138.b37.vcf:type=VCF -r DoxvsADAR3.out BAM_files/H2171_1_Dox_S1/H2171_1_Dox_S1_sorted.bam,BAM_files/H2171_1_Dox_S2/H2171_1_Dox_S2_sorted.bam,BAM_files/H2171_1_Dox_S3/H2171_1_Dox_S3_sorted.bam BAM_files/H2171_4_Dox_S1/H2171_4_Dox_S1_sorted.bam,BAM_files/H2171_4_Dox_S2/H2171_4_Dox_S2_sorted.bam,BAM_files/H2171_4_Dox_S3/H2171_4_Dox_S3_sorted.bam

I tried to remove the -f=V option but then complains that it needs the format specified.

java.lang.IllegalArgumentException: Cannot set a file type if the output is not to a file. at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.setOutputFileType(VariantContextWriterBuilder.java:185) at jacusa.io.format.call.VCFcallWriter.(VCFcallWriter.java:59) at jacusa.io.format.call.VCFcallFormat.createWriter(VCFcallFormat.java:41) at lib.worker.WorkerDispatcher.(WorkerDispatcher.java:43) at lib.util.AbstractMethod.getWorkerDispatcherInstance(AbstractMethod.java:63) at lib.util.AbstractTool.run(AbstractTool.java:59) at jacusa.JACUSA.main(JACUSA.java:96) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)