v6.0.0 - Efficient normal panel

Modified normal panel is now handled in more efficient way - makes BRASS GROUP step significantly faster.

If you have an existing -filter reference file you will need to convert it as described here.

v5.4.1 - Cytoband is required file now

Handling of retrieval of cytoband file is not feasible within the code. Users need to provide this on command line so that it is possible for code to be species/build agnostic.

Species Agnostic

pcf function in copynumber package is now species agnostic
removed NA rows before applying gam function

Edgecase fix

Two groups (1 reciprocal event) resulted in an case where the breakpoint resolution code fails to merge local events successfully.

Fix retains the event.

Handle very quiet data

Can occur when run on data where both samples are essentially normal - #51

v5.1.5

Fixes an environment variable.

v5.1.3 - Correct read collection

Improves methods used to select the reads originally contributing to the brassI group for the remapping tests.

no_reads should no longer be seen in the r5.scores file. Initial tests suggest an improved specificity and sensitivity.

v4.0.13 - R cleanup

Some issues with how file paths were being handled have been resolved, see #31.

Final filenames modified slightly to make clear which files incorporate data generated based on both input samples (primarily those files residing in output_loc/intermediates).

v4.0.12 - Much more stable

Resolves some output errors in VCF and improves stability further.

v4.0.0 - rework of filtering

Please be aware that the flow of processing changes in this release.