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Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view #2746
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Codecov Report
@@ Coverage Diff @@
## main #2746 +/- ##
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- Coverage 60.63% 60.23% -0.40%
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Files 566 571 +5
Lines 26348 26578 +230
Branches 6422 6472 +50
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+ Hits 15976 16010 +34
- Misses 10047 10243 +196
Partials 325 325
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this PR has a couple of extra changes now supports loading chain files (e.g. from UCSC) files to display synteny. this combo of
this covers a good amount of basic "whole genome alignment" formats this PR also...
example screenshot showing this liftover file https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz (reads it gzipped from the remote url) the import form for the dotplot and linear synteny import forms is redesigned to allow .delta, .chain, .paf, and .out files (mashmap) |
…t view Add delta file support Add delta track to yeast synteny Add delta adapter support
… e.g. hg19 vs hg38 chain file
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Fixes #1557
Fixes #2093
Adds a "comparative adapter" with PAFAdapter and DeltaAdapter. The PAFAdapter was in the dotplot plugin
Adapts some code from minimap2's paftools.js https://github.com/lh3/minimap2/blob/master/misc/paftools.js#L1853 (licensed MIT, cited in source code) to parse the delta file