vadimzalunin/crammer — Issue #3: runtime exception v0.3
Author: calkan
Created: 2011-10-31 20:24:13+00:00
State: open

Hi

I mapped one lane of human data (100bp PE; SRR034940) with BWA (default parameters), and sorted & indexed the BAM with samtools. Crammer gives an exception:

java -d64 -jar cramtools.jar cram --input-bam-file SRR034940.sort.bam --reference-fasta-file hg19.fasta --output-cram-file SRR034940.sort.cram

DEBUG CramWriter - Block purged: 100000	3961653	39.62	0.3962
Exception in thread "main" java.lang.RuntimeException: Illegal base at 60830533: 77
at uk.ac.ebi.ena.sra.cram.Utils.capitaliseAndCheckBases(Utils.java:207)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.getReferenceSequenceBases(Bam2Cram.java:150)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.compressAllRecordsForSequence(Bam2Cram.java:164)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.run(Bam2Cram.java:136)
at uk.ac.ebi.ena.sra.cram.Bam2Cram.main(Bam2Cram.java:296)
at uk.ac.ebi.ena.sra.cram.CramTools.main(CramTools.java:66)

thx.