The built in filter flag, -F, does not work.

[mrvollger]

The -F flag isn't working as intended for filtering bam records. As a workaround, users can do e.g.:

samtools view -F 2308 input.bam | ft fire - out.bam

instead of

ft fire -F 2308 input.bam out.bam

while I work on the real solution.