Merge pull request #546 from kern3020/master

fix syntax error
Add configuration for evaluating joint calling, platypus and SNAP. Small fixes to SNAP sorting memory usage to leave enough for alignment
add qsignature to main.py. Fix possible problems is qsignature doesn't run, and prepare to accept whole genome analysis
Pin cutadapt to version 1.5.
Fix single-end progress message for STAR.
Subsetting a gzipped FASTQ file for testing fixed.

It was outputting uncompressed FASTQ files that had an extension of
.gz. This fixes that behavior by adding a gzip file opener that
will do the right thing if it is a gzipped file.
Merge upstream changes
Merge branch 'lpantano-upstream'
Initial cancer calling evaluation using DREAM challenge synthetic dataset 3
Script to format DREAM truthsets into VCFs and BEDs to feed into bcbio-nextgen evaluations
Provide better estimation of batch sizes based on open file limits. Thanks to Nick Carriero for patch. Get list of contributors up to date
Workaround for sickle not handling 0-length reads added.

Just use cutadapt and write to temporary files for now, we'll
revert that switch when sickle is fixed.

Pin cutadapt to 1.4.2; 1.5.0 has some issues with file format
detection.
Improve Java memory usage for large numbers of tasks: use serial GC instead of parallel and slightly reduce GATK memory usage to stay within configured limits. #532 Thanks to @BioInfo @mjafin
Additional java scaling memory improvements for joint recalling and validation
Improvement re-run speed by avoiding overhead of copy.deepcopy during parallelization. Provide better hooks for cleaning up clusters during failure to ensure controller/engines removed
Use GATK CatVariants for concatenation to avoid issues with vcfcat and GATK multi-sample output. Fixes #547
Ensure genome_build treated as a string for numerical genomes. Thanks to Mark Rose
Enable validation on joint called samples. Ensure deepish_copy handles nested dictionaries
Use more evocative names for the alignment/qc checkpoint files.
add kraken to standard pipeline, fix bugs for kraken, and reducing memory for qsignature

more changes for kraken