Incompatibility with LINX v1.24 fusion output file

The LINX v1.24 release includes an additional column in the fusion output file, see this commit
Running gpgr.R linx on LINX v1.24 produces the below error
Possible fix also provided below

Click to show command and error

Command: ```bash docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/umccr/gpgr:1.4.4 \ gpgr.R linx \ --sample sample_name \ --plot data/plot/ \ --table data/linx_somatic/ \ --out sample_name_linx.html ``` Log of stdout/stderr: ```text ── Start rendering LINX R Markdown report! ──────────────────────────────────────────────────────────── processing file: linx.Rmd |.................... | 40% [fusion] Quitting from lines 171-175 [fusion] (linx.Rmd) Error: ! ncol(d) not equal to length(nm) Backtrace: 1. gpgr::linx_fusion_process(linx_path_tab("fusion")) 2. gpgr::linx_fusion_read(x) 3. gpgr:::linx_read_table(x, "fusion") 4. assertthat::assert_that(ncol(d) == length(nm)) Execution halted ```

Click to show possible fix

```diff diff --git a/R/linx.R b/R/linx.R index c1f3176..a74fa8e 100644 --- a/R/linx.R +++ b/R/linx.R @@ -132,6 +132,7 @@ LINX_DESCRIPTIONS <- tibble::tribble( "[KNOWN_PAIR, PROMISCUOUS_5, PROMISCUOUS_3, PROMISCUOUS_BOTH, EXON_DEL_DUP, ", "IG_PROMISCUOUS, IG_KNOWN_PAIR, KNOWN_PAIR_UNMMABLE_3 or NONE (if no match is found)" ), + "fusion", "reportableReasons", "c", "Reasons for given reportable status", "fusion", "phased", "c", "Set to 1 if a phased fusion can be formed (after allowing for exon skipping)", "fusion", "likelihood", "c", ".", "fusion", "chainLength", "d", "0 for simple fusions. If fusion is chained equal to the total length of segments chained between 5' and 3' partners", ```

I can submit a PR if you like @pdiakumis, up to you!

umccr / gpgr

Incompatibility with LINX v1.24 fusion output file #64