Denis C. Bauer

Implement extraction method for pair-wise interactions from the tree

2

From the JSON tree file extract pair-wise interacting features by making a pair-wise list and counting co-occurrence in the tree. Potentially weighting them by importance.

Create an automated way to spin up a Spark cluster on AWS with VariantSpark installed so researchers can get started easily. This extends the work done by Lynn Langit as...

Output trees in JSON format

1

Implement a readable output e.g. JSON for the trained trees. This will help evaluate the resulting interactions and visualise them.

VariantSpark extended to support continuous labels

1

VariantSpark currently only supports categorical labels. While binning continuous variables to use as multiple categories, is a workaround, fully supporting continuous labels would be preferable.

The current code is 40% covered by unit tests, the rest need to be added

SamVar

1

Samtools variant calling is not working anymore with samtools 1.1 [bam_rmdup_core] processing reference 16... Samtools-htslib-API: bam_get_library() not yet implemented /apps/gi/ngsane/devel_db//mods/samSNPs.sh: line 97: 1358176 Aborted samtools rmdup $f $OUTDIR/${n/bam/drm.bam} This is...