v1.1

JaBbA v1.1

This is a minor release of JaBbA, a framework for genome graph inference from bulk whole-genome short read sequencing.

This release enables the use of Gurobi for MIP optimization. Like CPLEX, Gurobi is a proprietary solver but offers a free academic license. To run JaBbA with Gurobi, you will need to install Gurobi and its R interface.

Then, run with the flag --gurobi TRUE:

jba ${JABBA_PATH}/junctions.vcf ${JABBA_PATH}/coverage.txt --gurobi TRUE

Please note that you may also need to install an updated version of gGnome which supports Gurobi.

Additional changes are detailed in the changelog below.

What's Changed

• save purity ploidy values to a table by @ShaiberAlon in #55
• transform with rel2abs before saving jabba.simple.png plot by @ShaiberAlon in #56
• read.junctions by @zining01 in #58
• fix jba missing default bug by @zining01 in #59
• Gurobi by @zining01 in #63
• fix bed file cov input and jba defaults by @zining01 in #60

Full Changelog: v1.0...v1.1