Provide explicit targets for minimum and maximum calling coverage and remove coverage_depth which was poorly defined and minimally used. Fixed #322
Remove pointers to coverage_depth in configuration inputs
Fix failure to install snpEff databases on new installations. Fixes #336
Correctly bgzip and compress in write_empty_vcf. Thanks to @lbeltrame. Fixes #338
Fix issue in coverage calculator with genes on '-' strand.
Revert combine_variant_files back to GATK instead of vcflib vcfintersect. vcfintersect not correctly handling many merge cases. Fixes #338. Fixes #339. Fixes #343
Use new gemini targets for testing and small files to avoid building gene tables during testing, which causes unit tests to slow down dramatically with gemini 0.6.5a. Thanks to @arq5x
Use MIT licensed GATK framework code for PrintReads and CombineVariants work, moving to GATK 3.0 codebase
Add ability to pass specific command line options from YAML configuration to FreeBayes.
Provide improved mechanism to add GATK jars into bcbio-nextgen. Handles updating version information in manifest and supports academic and commerical downloads. Fixes #332
Fix bug where filename was not shown in failed assertions.
Add target for only running multiple caller test. #340
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Eliminate memory issues using PrintReads in large concurrent runs by reducing memory usage. Ensure do.run subprocesses are cleaned and closed
Remove all references to removed max_errors parameter. Fixes #346
Ensure read groups correctly specified on bwa aln alignments. Fixes #346
Remove some cruft. Set STAR to be the default.
Fix for Tophat with single-end reads and final BAMfile naming.

In single-end mode, fixing the unmapped reads with single-end
reads was causing all reads to be discarded. Also the
final BAMfile was getting linked to from the align directory and
not the subdirectory of the alignment below it.
Put symbolic links in the correct directory.

These were inadvertantly linked in the toplevel align directory
instead of the lane-specific subdirectory.
Add a singleend tag for testing single-end data.