ArrayIndexOutOfBoundsException when converting cram to fastq

[anamijalkovic]

Hi Vadim,

I am trying to convert 1000genomes publicly available cram files to the fastq files and I get ArrayIndexOutOfBoundsException.

For example, for the following file: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA06984/alignment/
with following command line: java -jar cramtools/cramtools-2.1.jar fastq -I NA06984.alt_bwamem_GRCh38DH.20150526.low_coverage.bam.cram I get error message:

Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at net.sf.cram.CramTools.invoke(CramTools.java:93)
at net.sf.cram.CramTools.main(CramTools.java:123)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 57
at net.sf.cram.structure.Block.(Block.java:50)
at net.sf.cram.build.CramIO.readSAMFileHeader(CramIO.java:496)
at net.sf.cram.build.CramIO.readCramHeader(CramIO.java:314)
at net.sf.cram.Cram2Fastq.main(Cram2Fastq.java:94)
... 6 more

Could you please help me solve this problem.

Thank you,
Ana

[vadimzalunin]

Hi Ana,

The repository has been moved to https://github.com/enasequence/cramtools
Please try the latest version with cram3 support:
https://github.com/enasequence/cramtools/blob/cram3/cramtools-3.0.jar?raw=true

Vadim