Modified samples with 0 index to get converted to fastq, Added WIP index stats for reads 2 or 3.
Using NumCycles from runinfo.xml to get index_size. This is problematic though
Added: Moving R2/R3 index files to Undetermined_indices, Rename second read if any to R2
Changed: Merged Undemultiplexed.metrics files will now be sorted to accomodate indices as reads
Updated .travis.yml to remove outdated --use-mirrors pip argument (caused Travis builds to fail)
Merge pull request #290 from remiolsen/single_sample_on_lane

Single sample on lane
Update .travis.yml to --allow-external when finding pysam
Merge pull request #292 from mariogiov/master

Update .travis.yml to --allow-external when finding pysam
Fixed: get_bases_mask() will now handle all three 'classes' of base_masks/runsetups
Changed: Single-sample-on-lane indexes will now be renamed to I1 and I2 instead of R2..
Merge pull request #293 from remiolsen/single_sample_on_lane

Single sample on lane
Changed: Will handle 'NoIndex' indices
Changed: Moved illumina_finished_msg unittests to separate test file
Removed: paramiko dependency
Merge pull request #294 from remiolsen/single_sample_on_lane

Single sample on lane
Fixed: Should handle the unlikely event/mistake where only one read was sequenced
Merge pull request #295 from remiolsen/single_sample_on_lane

Single read sequenced
Fixed: Will demultiplex '0bp' indexes in a separate run to give correct demux_stats
Merge pull request #297 from remiolsen/single_sample_on_lane

Fixed: Read counts for samples on single lane
Run fastq-screen with only first read