Delfies

Fixes

- Bugfix: Handle no 'G2S' breakpoints
- Bugfix: Handle sequence extraction for negative start coordinates
- Bugfix: one-based error in sequence extraction coordinates

Features

Breakpoint detection now tolerates mutations in telomere arrays (in read softclips), via CLI argument `--telo_max_edit_distance`.

Features

* Granularity of clustering of adjacent breakpoints can now be controlled using newly-introduced `--clustering_threshold` CLI option
* `breakpoint_window` in the output file `breakpoint_locations.bed` now refers to all clustered breakpoint locations with >= `--min_supporting_reads`
* Removed `--cov_window_size` for looking at output `breakpoint_foci` - a fixed window is now always produced around each focus (=putative breakpoint location).

Features

* Added a `G2S` breakpoint detection mode
* Documented breakpoint types (S2G, G2S) in README

Features

* Functional 'S2G' mode: detection of breakpoints as telomere-containing softclipped-reads