add pindel
pindel integration as indels caller together with mutect
remove import and correct is_installed function
Remove merging of bed files in _subset_bed_by_region

Handle merging within variant callers if necessary (e.g. FreeBayes)
Added an option into bed prep to not merge overlapping regions. Useful for VarDict amplicon aware calling.
Update run_tests.sh

Handle paths with spaces.

The absolute path to bcbio_nextgen.py may have spaces, symlinks notwithstanding. In this case, dirname tokenizes the output of readlink as multiple strings, and this propogates to the last line of the script. Quoting suffices.
Merge pull request #611 from etal/patch-1

Handle paths with spaces in run_tests.sh
Remove mosaik reference from documentation. Thanks to @inti. Fixes #608
Updated joint validation comparison with samtools, update documentation
Do not attempt to retrieve VEP resources for Pseudomonas. Fixes #609
Avoid uploading discordant and split read output files to Galaxy data libraries
Ensure ensemble validation CSV summary correctly passed to upload. #604
Install ia32-libs so we can run 32 bit executables.
Revert "Install ia32-libs so we can run 32 bit executables."

This reverts commit bd0b1f9300a034b1bba79734b45193c234907ce5.

Fixed upstream in Homebrew in the cmake formula.
Merge pull request #602 from lpantano/upstream

pindel integration
Polishing custom genome creation.

Update .loc files and generate resource files when installing a custom
genome. Closes #580, #612.
Enable intersection based ensemble calling. Update tumor/normal ensemble to handle approach. Swap synthetic three example to use ensemble intersection approach, pindel and exon/intron refseq regions
Merge pull request #607 from mjafin/patch-5

Remove merging of bed files in _subset_bed_by_region
new format and new level for qsignature
new cutoff for full mode of qsignature