# 0.1.23

## What's New?
* Added `vf.pp.finalizingVerkkoFilletObj()` — a one-stop helper that finalizes a `VerkkoFillet` object by marking main contigs (`keepContig`), filtering short disconnected nodes (`checkDisconnectNode`), retaining nodes in unresolved gap regions (`keepNodesInUnresolvedGaps`), and refreshing connections (`updateConnect`).
* Added a command-line driver script: `src/verkkofillet/bin/automatic_script.py`. Runs the standard QC/assignment/telomere pipeline end-to-end given `--verkkoDir`, `--ref`, `--map_file`, and an optional `--internal_tel_threshold`.

## Key Modifications
* `vf.tl.convertRefName()` now produces a bgzipped FASTA (`*.rename.fa.gz`) and delegates the renaming to `changeChrName.sh` for consistent behavior with `vf.tl.renameContig()`.
* `changeChrName.sh` now supports gzipped input FASTA (auto-decompresses) and always emits a bgzipped, samtools-indexed output FASTA.
* `getChrNames.sh` now skips the mashmap step when `unitigs.hpc.mashmap.raw` already exists, avoiding redundant re-runs. The HiC-pipeline branch threshold was lowered from `$11 >= 50000` to `$11 >= 10000`.
* `vf.pp.find_intra_telo()` now returns a clean, fixed column ordering: `contig, distal-left, distal-right, internal-left, internal-right, problem, ref_chr, contig_len, ref_chr_len, hap, old_chr, completeness, hap_verkko, t2tStat`.

## Plotting
* Default saved figure format changed from PNG to PDF for `n50Plot`, `qvPlot`, `completePlot`, `contigLenPlot`, `contigPlot`, `showMashmapOri`, `nodeMashmapBlockSize`, `percTel`, `plotHist_readOnNode`, and `readOnNode`.
* Added a `force=False` parameter to the above plotting functions; when `True`, an existing figure file is overwritten instead of being skipped.
* All plot-saving calls now use `bbox_inches='tight', pad_inches=0.1` to avoid clipped labels.
* Suppressed noisy `fontTools` INFO logs in `_baseQC`.

## Fixes and Updates
* `vf.tl.renameContig()` now validates the chromosome map file and aborts with a clear message if `contig` or `new_contig_name` contains duplicates.
* Tutorial `how_to_run_verkko_cns.md` updated: clarifies that the final path file is `outDir/6-layoutContigs/consensus_paths.txt`, reminds users to confirm gap-filled paths are present, and notes that since Verkko 2.3 `--hifi`/`--ont` are auto-detected.