Stathis

Any timelines on this? Would you accept a PR e.g. for the GCcontent, LowComplexity and mappability tracks (which look straightforward) on this version of the genome for instance: ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz What's...

Might be related to this: `sambamba depth base -L chr22_KI270731v1_random:0-150754` gives `sambamba-depth: Conversion negative overflow` but this works: `sambamba depth base -L chr22_KI270731v1_random` same for any contig, I just chose...

Hi @pjotrp , sorry for the lack of response! This is still an issue (on my hands at least) with 0.7.1: `sambamba depth base -L chr22_KI270731v1_random:0-150754 NA12878-xxx.bam sambamba 0.7.1 by...

Ok I've narrowed down the bug. It seems to occur when the start coordinate is zero, e.g.: `sambamba-0.8.0-linux-amd64-static depth base -L chr1:0-10 any.bam` same for `region` I'm guessing it uses...

Yup that was what I ended up doing. I think https doesn't work because of firewalls and things... Thanks for your reply.

Thanks @daviesrob. I wonder whether there should also be a warning? (e.g. is there's a @PG tag in the bam header with the same seed). It certainly is not an...

thanks for the thorough explanation. That makes a lot more sense now. I think a warning based on the header would be the cheapest and reasonably effective, since samtools view...

Hi Chris, Thanks for this. I just wrote my first script in pyflow and I'm very pleased. Fantastic piece of code. A quick question: is there a way to clean-up...