Pjotr Prins

Glob

6

Globbing multiple documents. - [x] Fixed test that allowed 2 schemas to be passed in - [x] Multiple documents on command line - [x] Solve RDF compression because of shared...

Versioning with latest python libs

7

These versions pass on my Guix build. You may need to edit some.

Treat "./." genotype as valid

1

Freebayes comes up with "./." as a genotype. It probably means it can't score it(?). Bio-vcf needs to treat it as non-empty. Currently it sets everything to nil. "./.:145.222:44:27:885:13:378:-10,0,-10"

Use regex for sample names

1

Be useful to set regex on --ifilter-samples etc. for large multisample series.

A NoMethodError can show the variable that is nil by post-parsing the filter/eval string and testing the values. That would speed up eval debugging for users. r.tumor.dp>=20 and r.normal.dp>=20 and...

E.g. ``` ./bin/bio-vcf -i --num-threads 4 --thread-lines 4 --filter 'r.info.dp>2' < test/data/input/multisample.vcf|md5sum ``` may render different ordered output due to queue handling. The result is OK, but it is not...

We should make use of the new Ruby &. nil operator. Currently nils fail because it can mean either a missing value or a user mistake (unknown field). These sources...