0.1.23

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.

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