Seth

[tests] Read assingment and barcodes are never checked

1

https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/test/scala/com/fulcrumgenomics/fastq/DemuxFastqsTest.scala#L795 The `assignment` and `barcodes` are set up but never actually checked.

R session aborts when `Result::Err` is returned from Rust or a `panic!` occurs

1

Reading [this](https://github.com/extendr/extendr/issues/278) thread I'm lead to believe that extendr should notice a panic and convert it to an error message on the R side. But the in following example code...

In release mode doe a profile guided optimization pass like hck https://github.com/sstadick/hck/blob/master/pgo.sh This improves performance ~5-30%

Look into writing my own pileup engine

2

It would be nice to have Send / Sync built in all the way down.

This needs to be done in order to validate the "fast" term. I may way to do this till `in-depth` tool has also been added to benchmark all at the...

For example if a bedfile is missing you get this: ``` thread '' panicked at 'Parsed BED to intervals: No such file or directory (os error 2)', /opt/conda/conda-bld/perbase_1602523225266/work/src/lib/par_granges.rs:131:66 ``` Which...

Output more metrics in line with `bam-readcount`, but better formatted.

Add support of readgroup awareness and filtering

1

see sambamba depth

I'm looking to build a UTA database from a custom reference source (GFF / FASTA). Looking around the docs I wasn't seeing about how to go about doing this. I'm...

Release of 0.4.0

4

Hello! Is there a timeline for cutting the 0.4.0 release? Specifically I'm finding the `read_record_set_exact` functionality to be extremely useful.