## 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.