Updated documentation regarding resources: cores
Add bcftools based merge functionality that avoids issues involved with GATK file locks. Still needs full integration after further testing with isolated parallel merge functionality. #155
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add memoization for Cufflinks.
Fixed bug where very short files were not being extracted properly.
Added running bcbio-nextgen on a subset of test data.

test_run: True at the top of the sample configuration file
will downsample any BAM/fastq files to 10,000 entries before running
the pipeline.
test_run addition
Provide short filenames to merge and concatenate to avoid too long command lines with large numbers of input files
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Added Cufflinks output to the upload directory.
Added samtools sam->bam conversion and merging.

Part of phasing out of using Picard. sambamba is still flaky in a bunch of
areas so support for it is implemented, but turned off.
Revert the switch to samtools merge.

It doesn't work the same as Picard merge as it is.
Added memoization to FASTQ downsampling.
Run test_run downsampling in parallel.
Added quick option to downsample fastq files.

Just grabs the first N records.
Let sort_order detection work for BAM and SAM files.
Fixes to make Tophat more reliable.
Make alignment-post processing more reliable.
Remove commented out code.
Make Cufflinks output more verbose.