bam for consensus

[jdmontenegro]

Hi,

Does racon accepts bam files instead of sam files for the consensus calculation or do we need convert bam to sam in order to use it?

Cheers,

[rvaser]

Hello, sorry for the late response! Unfortunately, Racon only accepts SAM as alignment input. We will add BAM support in the new release.

Best regards, Robert

[claczny]

Hi,

thank you for the nice software! I understand that one of the focal points currently appears to be in accelerating racon using the GPU 👍

Nevertheless, I was wondering whether there has been any progress made on the BAM support already? I could not find anything related in the Changelogs of the Releases, so I am keeping my hopes low ;)

Best,

Cedric

[rvaser]

Hi Cedric, unfortunately no BAM support was added yet.

Best regards, Robert

[claczny]

I see and thanks for the quick reply!

Unfortunately, piping in the SAM file (as in https://github.com/isovic/racon/issues/9#issuecomment-275067339) appears to not be a solution either, as I get

[racon::createPolisher] error: file - has unsupported format extension (valid extensions: .mhap, .mhap.gz, .paf, .paf.gz, .sam, .sam.gz)!

I tried piping (samtools view -h alignment.bam draft.fna | racon reads.fastq - draft.fna) as well as process substitution (racon reads.fastq <(samtools view -h alignment.bam) draft.fna), both yielding the above error.

[rvaser]

Piping was removed since version 1.0.0.

[claczny]

That is good to know, albeit a bit sad :) I'll then just create a temporary SAM file from the BAM file. Should be fine too ;)

Thanks a lot!

Best,

Cedric

[sjackman]

Either reading BAM or piping SAM from samtools view is useful to me.

[rvaser]

I'll try to add it in the next refactor.

[sjackman]

I also use GZIP compressed SAM a fair bit, but BAM would be sufficient.

[rvaser]

Gziped SAM files are supported, but without piping.

[rvaser]

Accidentally pushed the wrong button :D

[sjackman]

Gziped SAM files are supported, but without piping.

Good to know!

[rvaser]

All formats that Racon accepts can be gziped.

[sjackman]

Gzipped BAM file? 😈 (just kidding, please don't)

[sjackman]

Actually a little-known fact that I've actually found really useful is that a BAM file is a gzip file. You can gunzip -c a BAM file to get an uncompressed BAM file. gunzip -c alignments.bam | samtools view works as expected.