vadimzalunin/crammer — Issue #8: Exception in thread "main" java.lang.NullPointerException when no --reference-fasta-file is specified
Author: ghuls
Created: 2012-01-02 16:17:30+00:00
State: open

Exception in thread "main" java.lang.NullPointerException when no --reference-fasta-file is specified

$ java -jar cramtools.jar cram --input-bam-file ./PEER-rg.bam --output-cram-file ./PEER.cram
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.reference.IndexedFastaSequenceFile.canCreateIndexedFastaReader(IndexedFastaSequenceFile.java:118)
at uk.ac.ebi.ena.sra.cram.Utils.createIndexedFastaSequenceFile(Utils.java:370)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.init(Bam2Cram.java:114)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.main(Bam2Cram.java:445)
at uk.ac.ebi.ena.sra.cram.CramTools.main(CramTools.java:55)