bigdatagenomics / lime

Distributed Set Theory for Genomics

Lime

Getting Started

Building from Source

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

lime's Issues

any docs?

It would be nice to have any docs to understand how to use it

Improve test coverage for current code

Refactor package names to remove underscores

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

Do not enforce strandedness by default on Merge

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.

Command line classes should use loadFeatures and save/writeTextRdd

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.

Update pom.xml with proper dependency versions and exclusions

Serialization stack overflow on Merge calls

Kryo Serialization issue involving the serialization of objects in the recursive call of SetTheoryWithSingleCollection.

Implement Cluster

Implement cluster as bedtools does.

http://bedtools.readthedocs.io/en/latest/content/tools/cluster.html

Update ADAM dependency to 0.25.0

Complement command is currently not implemented

https://github.com/bigdatagenomics/lime/blob/master/lime-cli/src/main/scala/org/bdgenomics/lime/cli/Complement.scala#L56

Closest command is currently not implemented

https://github.com/bigdatagenomics/lime/blob/master/lime-cli/src/main/scala/org/bdgenomics/lime/cli/Closest.scala#L56

Create ASCII logo for LimeMain

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.

Bump to ADAM 0.23.0

Merge implementation performance

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.

Closest Implementation

Implement closest.

Add license and license headers to source files

Implement Subtract Functionality

Implement subtract functionality according to bedtools implementation:

http://bedtools.readthedocs.io/en/latest/content/tools/subtract.html