You will need to have Apache Maven version 3.1.1 or later installed in order to build Lime.
$ git clone https://github.com/bigdatagenomics/lime.git
$ cd lime
$ mvn install
Distributed Set Theory for Genomics
License: Other
You will need to have Apache Maven version 3.1.1 or later installed in order to build Lime.
$ git clone https://github.com/bigdatagenomics/lime.git
$ cd lime
$ mvn install
It would be nice to have any docs to understand how to use it
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
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.
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
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.
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.
Implement closest.
Implement subtract functionality according to bedtools implementation:
http://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
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