Rsamtools

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CRAM support - why not?

5

It appears CRAM is not supported by Rsamtools. I wonder why is that? Samtools support CRAM natively, so I would naively expect this should be a trivial task, no? This...

pd3

Right now `seqinfo()` returns a Seqinfo object with no genome information, even though that information is available in the file (the genome assembly is specified via the `AS` tag found...

hpages

Any chance Rsamtools will support CSI indexes anytime soon? We have a genome with multigigabase size chromosomes and many R packages cant support it ultimately because they rely on Rsamtools...

diego-rt

Add code of conduct

1

It may be worthwhile to add the Bioconductor Code of Conduct to this repo. Created using `biocthis::use_bioc_coc()`.

bschilder

Rsamtools with multiple threads?

2

Hi, can Rsamtools run with multiple threads? Thanks!

junjunlab

mtmorgan

Bug in scanTabix

4

Hi, I came across a bug in `scanTabix` where no data is returned when requesting regions on double-digit chromosomes (ie >chr9). This only appears to be an issue on Windows...

timoast

Rsamtools::pileup counts overlapping paired-end reads twice

5

Is there a way to disable this behavior?

alkodsi

Error with getSeq from opened fasta file (Rsamtools 2.0.2)

7

Hi, I am using Rsamtools 2.0.2, and I have faced an issue on reading sequences from fasta files. My issue is similar to https://github.com/Bioconductor/Rsamtools/issues/5 , but not exactly. When I...

farshadf

min_nucleotide_depth parameter of PileupParam doesn't take 0

1

Hello If a user wants all positions output even if a reference position has zero coverage, the min_nucleotide_depth parameter=0 does not work to output the position with zero coverage. p_param

sarahwajid