0.1.18

0.1.18#

2025-03-05

Key modification#

  • vf.pp.searchNodes() function reports the total number of supported ont reads with collapsing the two direction of paths. For example, >node1<node2 and >node2<node1 will be reported together with sum of the number of total supported reads.

  • vf.pp.searchNodes() has a new parameter, multimap_filter, allowing the function to filter out multimapping reads and retain only the one with the highest MAPQ or a user-specified option.

  • vf.pp.find_intra_telo() reports not only the existense of interanl telomere of each contig, but also with proportion of the telmere sequences within each window.

  • vf.pp.calNodeDepth() function return FilletObj with node and edge attribution, which are new.

  • vf.pp.detectBrokenContigs() function.

  • vf.tl.mapBetweenNodes() function can pairwise aligning between nodes to find homologous nodes between haplotype.

  • The format of obj.gaf and obj.paths_freq are totally different from earlier versions. So please rerun vf.pp.readGaf() and vf.pp.searchNodes() with force=True to overwrite them.

Something new!#

  • new attributes inside of FilletObj, node and edge

  • include data directory under src, which have rDNA sequences and example dataset.

  • vf.pp.mkCNSdir(obj, new_folder_path, missingEdge=True) includes missingEdge paramter to build consesnsus directory for the assembly which have new nodes generated during gap filling.

  • vf.pp.connectContigs function.

  • vf.pl.percTel function to show the internal-telomere sequences.

  • vf.pl.n50Plot() function to plot N50

  • vf.pp.deleteGap()

  • vf.tl.gfaToFasta() can convert gfa to fasta file.

  • vf.pl.nodeMashmapBlockSize() shows which nodes are the homologous nodes of given node.

Fixed or edited!#

  • fix vf.tl.rmrDNA() function to include rDNA_sequence param.

  • fix vf.tl.insertGap function and integrate it to the basic tutorial

  • vf.pp.writeFixedPaths(obj) could handle startMarker and endMarker which are generated from new function ``.

  • vf.pp.highlight_nodes() function will grep correctly.

  • vf.pp.fillGaps() function has notes parameter.

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