Mark Diekhans

toil stats is way slow

4

this is on a smalish cactus run (10 mammals) I``` NFO:toil.utils.toilStatus:Traversing the job graph gathering jobs. This may take a couple of minutes. Of the 145093 jobs considered, there are...

Improve documentation of debugging pipelines.

2

Users moving to Toil will often have no experience debugging in a cloud environment. There needs to be a chapter on how a user approaches debugging. print and pydb don't...

document rationale for sample id being associated with ReadGroup

6

See #652 https://github.com/ga4gh/schemas/pull/652#discussion_r70047549

ReadAlignment, Variant, and Feature link to Reference by name rather than id

3

The design pattern in the API is that object linkage is done by id, not by name. The Position object uses referenceName rather than referenceId. This should be corrected or...

Cancer virus and human decoy search use cases not supported

1

One cancer use case is to mapping reads to both human and viral reference genomes simultaneous to detect the presences of viral DNA or RNA in samples. A similar use...

reads Program id definition inconsistent with rest of API

1

The Program record id field /src/main/resources/avro/reads.avd is defined in a manner inconsistent with the rest of the API: /*\* The user specified ID of the program. */ union { null,...

Error response need precise definition

9

The expected error responses from the API need precise definition to allow implementing consistent behavior between server.

A goal of the GA4GH sequence annotation API was - The annotation API needs to also be flexible enough to handle multiple references in the same gene or transcript. This...

If one goes to the github repo, one has no idea what MASH actually does from the README

A collaborator accidentally left one of the `-' off of an option like this: ``` gffread --ids H0C.ids -gtf isoforms.gtf > H0C.gtf ``` and got the deceptive error message: ```...