Hi Dylan, On Tue, May 21, 2019 at 02:32:48PM +0200, Dylan Aïssi wrote: > Control: severity -1 serious > > Hi, > I have tested the testsuite with the upstream binary (FastQC 0.11.8) > and there is no error, so the testsuite is fine. This bug was probably > hidden before we added the test of bam and sam files. Currently, > fastqc from our package is unable to process bam and sam files which > is very annoying for Buster. I guess we have to modify > htsjdk-api.patch, but I admit I have no clue how to fix it. The > easiest way should be to add SAMFileReader like suggested in [1]. Any > suggestion?
Thanks for pointing out this issue. No better suggestion than the naive one that I gave in issue #767. May be FastQC contacting upstream is a good idea. Kind regards Andreas. > [1] https://github.com/samtools/htsjdk/issues/767#issuecomment-264843094 -- http://fam-tille.de