Compressed output

[BrianLohman]

Hi,

I am using bazam to convert CRAM to FASTQ and it is working well. However, it would be very helpful if the output was gzip compressed. Would you consider adding this? It would greatly reduced disk space needed while working on AWS.

Thanks

[fcgportal]

You can pileup the interleaved fastq from Bazam into reformat.sh and output separated paired fastq.gz files. It works fine for me.

java -jar build/libs/bazam.jar -bam test.bam | reformat.sh int=t in=stdin.fq out1=out_r1.fastq.gz out2=out_r2.fastq.gz