Add documentation for presentations, slides and links
Fix typo in presentation links
Provide metadata target to specify sample sex and use to refine ploidy and final reported sex chromosomes. Correctly handles mitochondrial as well as X, Y. Fixes #33
Added file transaction to cutadapt.
Merge pull request #161 from mariogiov/recursive_shell_expansion

Recursive config file traversal to expand all shell variables
Explicitly update configuration when recursively setting paths; avoid relying on implicit dictionary updates #161
Remove mapping quality flag for FreeBayes. This is taken into account by default in recent versions: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/#comment-1495
Identify and avoid calling on extreme high coverage regions. These are found due to mapping problems in repetitive regions and contribute to long run times and errors in variant calling
Avoid low coverage and poor mapping quality annotations when using CallableLoci. These are not used for selecting regions and are better left to the downstream variant caller to annotate
Fixes for detecting excessive coverage: avoid downsampling below mazDepth value, avoid filtering by mapping and reporting low map quality
Ensure that shared excessive coverage regions are removed from final set of callable regions to avoid processing in super deep repetitive regions
Use union of excessive coverage regions for a group to avoid repetitive regions during population calling
Ensure multiplier and maximum multicore options pass through when using multiprocessing locally. Avoid overscheduling cores for individual processes when using single cores. Thanks to Zhengqiu Cai
During varscan run, write mpileup file to check for empty output files that cause VarScan to hang. Fixes #156
Cleanly handle BAM files into template generation without run group sample information
Handle batch calling of structural variants, explicitly sorting batches for sv callers that support them
Handle calculation of excessive coverage regions when none found in input. Provide ploidy estimates when no metadata present in configuration
Initial framework to support cn.mops CNV calling
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Subset analysis regions by chromosomal section, ensuring that internal regions truncate at the end of the overall chrom/start/end section. Replaces custom code with pybedtools for intersections