Additional fixes for *.loc parsing using tool_data_table_conf: handle mixed spaces and tabs and fall back on remapping approaches correctly
Do not fail on non-GATC reference or variant bases. These will pass through unchanged without attempting to swap strands, but will no longer error out. Fixes #81
Avoid reading entire file when finding samples to exclude
Handle complements for multiallelic SNPs. Fixes #81
Handle simultaneous symlinking of results on distributed runs
Provide more useful error message with multiple jars in configured directory. Fixes #76
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Correctly handle relative tool and data directory paths during installation. Fixes #82
Provide initial hooks to calculate coverage summary statistics for BAM files using bcbio.coverage. Provides a high level summary of coverage per genes of interest or all transcripts
Remove from ZeroMQ logging errors that silence logging
Ensure build parameter passed along to coverage assessment to allow contig remapping
Remove requirement for bcbio_system at the command line, detecting from automated install location if not specified. Improve documentation for getting started running the pipeline
Move whole genome example above exome since it runs directly without additional novoalign license
Bug fix for merging BAM files with bamtools: sort after merge since order is not maintained and avoid duplicates from noanalysis by better subsetting with bedtools
Bug fixes: correctly detect versions on GATK nightlies (#84) and allow skipping of incorrectly configured coverage without dropping samples
Release v0.7.1 and include better documentation on configuring
Default points to /usr/local/share instead of /usr/share.
Added Tophat2 as a _tool.
Point to bowtie2 genome locations.
Bump to next development version