gatk

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In debugging Java 17 issues with the docker tests, I noticed some lines in the Docker file were missing the append i/o redirection that I assume was intended to be...

cmnbroad

To-do's for CompareReferences and CheckReferenceCompatibility: CompareReferences * add functionality to run base-level comparison modes on specified sequences (not just detected mismatching sequences) * add option to ignore case-level differences in...

orlicohen

GATK should warn the user when the temp dir is "noexec"

2

As reported recently by Eric Jones: "Many newer Linux distributions will mount /tmp with the noexec mount option. If /tmp is noexec, then any JNA code (Java code that extracts...

droazen

SplitNCigarReads.java - retain original read name somewhere for split parts of reads so we know where it derived from.

4

## Feature request ### Tool(s) or class(es) involved src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java ### Description Modification requested. When splitting a read based on the spliced RNA cigar (N cigar symbol), the new split read...

brianjohnhaas

Very few changes strictly required, only a couple of package names changed. I did add some tracing as I was struggling to figure out what the problems were without this.

mcovarr

Gg vs 887 streamline vat tsv extract

10

gbggrant

Vs 778 spike import limit

1

The starting code for pushing through our 10k import limit. For reference @RoriCremer No need to actually review it. Just wanted to point you toward its existence in a useful...

koncheto-broad

Ah rate limit ingestion

1

Adding in a configurable delay after writing a batch of data to BigQuery

koncheto-broad

log4j minor bump to 2.17.1

1

per https://github.com/broadinstitute/gatk/pull/7624

calbach

SNVQ recalibration for flow based reads

1

ilyasoifer