Delfies v0.11.0

Features

• Added a telomere_addition.tsv output TSV to record what kind of template nucleotide, and telomere unit, gets added at breakpoints
• Added --sample_name option at CLI to process/compare multiple samples

Fixes

• [For developers] Intervals are now BED-like: [0-based inclusive, 0-based exclusive)

Delfies v0.10.0

Features

• Added a CLI option to keep breakpoints occurring in telomere arrays (in both S2G and G2S modes). By default, these are discarded. Addresses #9

Fixes

• Bugfix: lowercase nucleotides in genomes are now supported (Thanks @andrewhsiao11!)

Delfies v0.9.0

Major change is we now better deal with telomere arrays (in genomes and in reads)

Features

• Added clustering of contiguous, and/or overlapping telomere arrays, occurring in genomes

Fixes

• Fix #6: some S2G breakpoints were extensions of genomic telomeres, and thus false positives - these are now no longer included in the output breakpoint_locations.bed
• Bugfix: some G2S breakpoints were false positives as the softclips in the reads contained telomeres that were sometimes not detected - now fixed, with tests.

Delfies v0.8.0

CI

• Added automated PyPI release deployments
• Added a publically-available test dataset, described in the README
• Added integration test; this increased test coverage to 73% of the codebase

Delfies v0.5.0

Fixes

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

Delfies v0.4.0

Features

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

Delfies v0.3.0

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).

Delfies v0.2.0

Features

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

Delfies v0.1.0

Features

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