Merge pull request #3 from fwip/master

Link Undetermined indices for nextseq
Fix error when count type not found in API
Add multiple matching counts to bamcounts script
Hide qsub logs for fastqc only jobs
Correct check for bigwig filename in bwa paired trimmed process
Fix 0.0% dup scores

Picard apparently can't handle it when we've stripped the R2 reads
from the R1 reads in a BAM file.  If we convert it to BAM and back,
we can keep using Picard while stripping out the information that
keeps it from working
Standardize nextseq symlink ordering

In some cases, glob.glob() returns stuff off the filesystem in a
non-sorted order. This meant that L001_R1_003 didn't necessarily link to
L003_R1_001. This didn't affect anything downstream, but adding sorting
makes it behave more as you'd expect.
Fix error for lanes with no alignments

If a lane has no alignments, should just return and not create a script
instead of crashing
Merge pull request #4 from fwip/fix_nextseq_ordering

Standardize nextseq symlink ordering
Merge branch 'master' of github.com:StamLab/stampipes
Improve process paired BAM by turning more targets into changeable variables
Use the correct samtools fai option; this means older BAM files will need to be resorted
Short script to check BAM ref order status
Create picard hist file off INSERTMETRICS variable name
Make sure original BAM file is always indexed, continue improving variable usage
Sync spot-Rboth method with spot-R1 method
Fix for '_' to '-' replacement in bcl2fastq2