Use brew list as backup when brew which fails. Fixes #226
limit inclusion of fastq/bam files in input dirs

it's just a suggestion

moving forward, I wonder what's the best way to handle template creation for standard bcl2fastq output where fastq of each sample is kept in a single folder and the fastq files are split for every x number of reads
Workaround for pysam 0.6 header parsing issues.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Return a string instead of a list.
provides a simpler way to identify pairs 

handle uses case like:
12878_GAAACC_L001_R1_004.fastq.gz
12878_GAAACC_L001_R2_004.fastq.gz
12878_GAAACC_L002_R1_004.fastq.gz
12878_GAAACC_L002_R2_004.fastq.gz
12878_GAAACC_L002_R1_005.fastq.gz
12878_GAAACC_L002_R2_005.fastq.gz
Allow --fusion-mode to be set.

Also refactor to remove some of the bad logic and old code that
had accumulated.
Use do.run properly.
Add fusion_mode as an allowable 'algorithm' field.
Remove confusing hybrid_bait/hybrid_target options from configuration. Fixes #227
Added read length estimator.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Merge pull request #229 from tanglingfung/patch-4

provides a simpler way to identify pairs courtesy of @tanglingfung
Remove unused import.
STAR support enabled.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added resources for STAR.
Added fusion_mode support for STAR.

Also set a flag to make STAR to set the XS flag so it works
with Cufflinks.
Merge pull request #228 from tanglingfung/patch-3

limit inclusion of fastq/bam files in input dirs
Explicitly error out on samtools 0.19/bcftools 0.20 incompatibility. Avoid samtools in testing until new calling method finalized