Release Notes, Updates

Recent developments

DegNorm R package is out: http://bioinfo.stats.northwestern.edu/~jzwang/DegNorm/DegNorm.html
Added logic in reads.chromosome_coverage_read_counts method to search for requisite coverage and read count files before attempting to compute. This lets users who had DegNorm runs that died in the middle of coverage/read count computations start from where they left off. This is not the same as using a warm-start directory, which begins a DegNorm run beginning from the point after every (sample, chromosome) coverage/read counts have been computed. This fix addresses issue #30.
Added explicit checks that gene_id or gene_name tags appear in .gtf attributes. If a gene is found to have a missing required tag, pipeline gives more clear error message.

DegNorm accepted to Genome Biology! Read the paper.
Accounting bug fixes: correctly use pysam-loaded .bam files as 0-indexed.
Separate read counting for genes with mutual overlap vs. isolated genes.
In coverage_read_counts save parsed counts, coverage to disk instead of returning complex file tree dict.
Don't drop genes just because they may have a sample with 0 coverage.
Add notes about 0-indexing (for .bam files) and 1-indexing (for .gtf files) to docs.

Improve upon memory efficiency in coverage.gene_coverage - now sparse chromosome-wide coverage matrices are diced into approximately equally-sized chunks so that the dense versions of the coverage chunks are approximately ~0.5Gb memory, instead of calling .todense() on a whole chromosome's coverage matrix.
Enlist HTSeq package in .gtf file parsing to speed up identification of genes with intersecting exons. GeneAnnotationProcessor now single-process, much faster.
GH Readme points to DegNorm homepage.

degnorm_mpi entrypoint available for distributed pipeline runs.
change -c (cores flag) to -p (processes per node flag) to reflect that degnorm_mpi runs processes within a node.
Update install.sh so that if mpiexec is in PATH, automatically install mpi4py, otherwise don't.
Update installation documentation to reflect MPI requirements to run degnorm_mpi.

First release of DegNorm as a package.
degnorm entrypoint is the only supported CLI tool
get_coverage_plots and get_coverage_data are the only supported posthoc analysis tools