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elsiklab / gccontent

A JBrowse plugin for plotting GC content and GC skew
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Could it be updated to use bgzipped FASTA? #8

Closed billzt closed 5 years ago

billzt commented 5 years ago

Since 1.15.4, JBrowse could use bgzipped FASTA as reference files.

cmdcolin commented 5 years ago

As far as I could tell this is allowed automatically

{
   "formatVersion" : 1,
   "refSeqs" : "seq/volvox.fa.gz.fai",
   "tracks" : [
      {
        "storeClass" : "JBrowse/Store/SeqFeature/BgzipIndexedFasta",
        "type": "GCContent/View/Track/GCContentXY",
        "label": "GC Content",
        "urlTemplate" : "seq/volvox.fa.gz"
      },
      {
         "category" : "Reference sequence",
         "faiUrlTemplate" : "seq/volvox.fa.gz.fai",
         "gziUrlTemplate" : "seq/volvox.fa.gz.gzi",
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/SeqFeature/BgzipIndexedFasta",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/volvox.fa.gz",
         "useAsRefSeqStore" : 1
      }
   ]
}
billzt commented 5 years ago

Wonderful! Suggest to update README.md to let more people know about it.