JBrowse2: Speed up paf tracks with new tabix pif adapter. #1513
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…m/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone.
…ply to all future generated tools :)
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq
…dio replacement...
some prompts add bgperpx - todo add as a parameter
Add wiggle track colour and other controls Add bpPerPx in advanced section to control view scale at default open Clarify dependence on remote URI tabix data if uri source used.
still passes tests - no breakage yet.
…orking! Involved a substantial simplification of the default_session setup - just needed "configuration": displayId in the display. Simples.
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
…es tool and to the advanced control form.
fix biotools jbrowse entry informative error message if collection has no fasta reference
makes them much more useful for most purposes - can swap back otherwise local differences can appear to be more important than they really are... use element_identifier for labels instead of name
remove now missing specific wolf file from 3 old tests.
fix tool test output counts to match new code
… tracks GMOD/jbrowse-components#4583 Have updated vcf and blastxml test files too FWIW
…ls to avoid them becoming broken paths. For example, vcf sort adds a : to the name and that breaks the track path.
…ound like when failing on vgp.org pulsar.
…ated for vgp.usegalaxy add a failsafe so if the dependency javascript cannot be found it uses JBrowse to bootstrap itself.
File is named "bw/m:e.r.l .i-n.bw" Test finds <has_text text="me.r.l.i-n.bw_0"/> to confirm that ':' and ' ' have been removed
If local paf, index and use the tabix adapter If URI, check if the extension is paf.gz and use tabix if so otherwise use unindexed paf adapter
couldn't get the inbuilt thing working in biocontainers testing. no idea why.
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Thanks! You should at some point start with a frash branch :-) |
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oh - yes - this is old. Thanks - will do... |
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@bgruening: Dotplots use unindexed PAF format files at present and having spent some time exploring these very interesting artifacts, they can be big, too slow to load and frustratingly slow to refresh after adjusting the view....
JB2 has a new "PairwiseIndexedPAFAdapter" adapter using tabix indexing so have made that the default for local PAF sourced tracks to make it faster for range requests on large PAF files. The remote URI handling is more complicated and assumes it is tabixed index only if it ends in pif.gz or paf.gz - not predictable unfortunately - otherwise it is an unindexed remote paf.
The first test has been adjusted to confirm that the PIF adapter is in play and that the tabix files are present.
Black has reformatted some code again so the diff is annoying - sorry.