Nils Homer

Support variable length umis

2

Solves: https://github.com/fulcrumgenomics/fgbio/issues/557

Adding some classes to store chain files.

1

TODO: tests!

Add an option not to redirect error in DnaFoldPredictor

3

@tfenne something that has bugged me for a while, especially if I am creating many threads to run vienna rna

Allow fgbio tools to access meta information about themselves.

2

This allows SAM program records to be created.

Adding in options to DemuxFastqs for asynchronous reading and writing

2

* Added the --async-reading option to specify if and how to perform asynchronous reading of the inputs * Added the --num-writing-threads to specify if and how many threads to use...

Optionally extract/annotate the UMI qualities in addition to the UMI bases in the following tools: - [x] `AnnotateBamWithUmis` (see #733) - [ ] `ExtractUmisFromBam` - [x] `FastqToBam` (see #740) -...

The various `Update*ContigNames` tools may require sorting after run. Wouldn't it be nice if they sorted the data for you? - `UpdateGffContigNames` - two levels of sort, by contig only...