Sascha Steinbiss

GFF3 validator should not stop on first error

1

Currently, the GFF3 parser stops on and outputs only the first error encountered in the input. For automated use, e.g. in a GFF/Git-based annotation tracking system, it might be convenient...

Weird booleans in Ruby bindings on Mac OS X

2

Boolean values returned from C function calls are unpredictable on Mac OS X if they are checked for being equal/different from 0/1, probably due to 64/32-bit issues. Try using the...

'gt seqlensort' test fails on Mac OS X

5

Apparently on Mac OS X the encoded sequence output from 'gt seqlensort' causes a different 'gt encseq info' output than the one from 'gt encseq encode', causing a test to...

Currently, `Derives_from` is handled just like any other attribute. But in reality it, much like the `Parent` attribute, is part of the graph structure definition and references the ID of...

Implement Tabix support for FeatureIndex

3

Tabix (http://bioinformatics.oxfordjournals.org/content/27/5/718) is a generic indexing library for genomic regions. We should investigate its use as a persistence back-end for the GtFeatureIndex as it is expected to be way faster...

Test reference results not portable across architectures

3

Debian runs the testsuite (`make test`) during the build process for its Augustus packages. While building packages for non-amd64 architectures (see list at https://buildd.debian.org/status/package.php?p=augustus), we noticed that builds were failing...

Add example compaction configuration

11

This PR adds an example configuration for the compaction plugin, affecting Suricata data. ### :memo: Checklist - [n/a] All user-facing changes have changelog entries. - [n/a] The changes are reflected...

-subStruct does not print nested fields in array items

1

I'm trying to use gojson to generate structs for an array of items, which may or may not contain (disjunct) keys with different sub-objects. Example (let's call this `test.json`): ```json...

Please use consistent license

2

It looks like the license headers still show different licenses, some GPL: ``` $ git grep -l 'GNU General Public Licen' peframe/modules/dump.py peframe/modules/info.py peframe/modules/loadfile.py peframe/modules/pecore.py peframe/modules/secalert.py peframe/modules/stdoutput.py peframe/modules/strings.py ``` and...

Hi, I'm looking to package peframe for Debian and in order to automate checking for new versions, etc. it would be nice if you could tag released versions using Git...