Brent Pedersen

@ulazcanoCICbioGUNE I think you'll need to decompress `/Genomes/Ref_genome/Homo_sapiens.GRCh38.dna.primary_assembly_110.fa.gz` and then re-run the indexing with `bwameth.py index /Genomes/Ref_genome/Homo_sapiens.GRCh38.dna.primary_assembly_110.fa`

you could try: ``` touch Homo_sapiens.GRCh38.dna.primary_assembly_110.fa.pac touch Homo_sapiens.GRCh38.dna.primary_assembly_110.fa.amb ``` to make sure their mod times are newer than the .fa file.

you could comment out that check in bwameth.py

Hi, it uses the sam flag to determine primary and it only counts primary, not secondary or supplemental reads.

I don't have the cycles to add this now, but this should be reasonable to add, see the function `convert_fasta`. I think you'd convert the complement of the reference and...

thanks for the careful description. I don't intend to fix, but will accept a PR that does. I think that would also require manually setting the addition of the RG...

if you set `reference=/path/to/some.fa` then do: ``` bwameth.py index $reference bwameth.py --threads 16 --reference $reference ... ``` then it will work. you don't pass the .c2t file.

can you update to the latest bwameth.py so we are on the same version? the new version just outputs sam.

I would recommend to find out if there's a module you can load on the cluster that has python2.7. If not, I would install conda in your $HOME and work...

Hi, thanks for reporting. What if instead of the if block you do: ``` res.decode("utf-8", "replace") ``` ?