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License: Other
Distributed Set Theory for Genomics
License: Other
The hack that currently exists for the merge implementation is extremely slow and contains a significant amount of ListBuffer
manipulations.
This is blowing up memory and runtime.
Java and scala package names don't usually contain underscores.
I'd propose
org.bdgenomics.lime.set_statistics → org.bdgenomics.lime.statistics
org.bdgenomics.lime.set_theory → org.bdgenomics.lime.theory
Kryo Serialization issue involving the serialization of objects in the recursive call of SetTheoryWithSingleCollection
.
Implement cluster as bedtools does.
http://bedtools.readthedocs.io/en/latest/content/tools/cluster.html
It would be nice to have any docs to understand how to use it
Following the Bedtools defaults.
http://bedtools.readthedocs.io/en/latest/content/tools/merge.html
We should add separate classes for strandedness enforcement and unstranded merge.
All of the command line classes could use loadFeatures
instead of loadBed
to handle all the different feature formats that ADAM supports, and FeatureRDD.save
or TextRddWriter.writeTextRdd
as appropriate for writing to disk.
Implement closest.
Implement subtract functionality according to bedtools implementation:
http://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
See
http://www.patorjk.com/software/taag/
Or maybe a logo?
.;++
;++#
+++#
+##.
ooooo+oo
oddoossssshM
Ms++ssssssdsm
Ms+ssssssyydsM
MsssssssyyddsM
mssssyyhhdhsM
Mshhhhhhhddo
oo+ooooo
Might have to squint. A lot.
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