Preparation for Phylo++

v1.0-rc2

Merge branch 'master' of https://github.com/morrislab/phylowgs

SMC-Heterogeneity Release 5

Numerous improvements over last eight months.

PhyloWGS v1.0-rc1

This is the first release candidate for PhyloWGS v1.0. This version is underlying our analysis of thousands of tumors as part of the Pan-Canacer Analysis of Whole Genomes project, in which it has been stable and robust.

If you're using a prior version of PhyloWGS, in addition to pulling the latest code from GitHub, please recompile mh.o via the command listed in the README:

    g++ -o mh.o -O3 mh.cpp  util.cpp `gsl-config --cflags --libs`

SMC-Heterogeneity Release 4

• Batch IO operations. Makes massive performance difference when running on network filesystem.
• Suggest using -O3 flag when compiling. Recompile mh.o to take advantage of this via the command g++ -o mh.o -O3 mh.cpp util.cpp gsl-config --cflags --libs``.

SMC-Heterogeneity Release 3

Fix CNV parsing for SMC-Het format.

SMC-Heterogeneity Release 2

Second release intended for use in the SMC-Heterogeneity Challenge.

SMC-Heterogeneity Release 1

First release intended for use in the SMC-Heterogeneity Challenge.