V3LOOP alignment

The big change is to switch V3LOOP to align using Gotoh pairwise alignment before using bowtie2 mapping (#370).

Other changes:

• Sweep deletions together, and align to codon boundaries (also part of #370).
• #366 - Put all of HIV on a single seed.
• #394 - Add resistance reports to BaseSpace version.
• #357 - Valid reads threshold for G2P report.
• #314 - Report dashes in consensus for low coverage areas.
• #383 - Miseq monitor handles expired Kive sessions.
• #315 - Report cascade of data through the pipeline.
• #386 - Convert pipeline to Python 3.

Trim adapter sequence

The main improvement is #312, trimming adapter sequences from reads. This reduces a lot of the soft clipping displayed in coverage maps, and improves the HCV genotype detection. Other changes were mostly to improve stability. See the milestone for a complete list.

Improved Reporting RC2

Fix error handling in MiSeq monitor, and correct some key positions of NS3.

For the full list, see the milestone.

Improved Reporting RC1

The main change in this release was to add several lines to the coverage reports: #313 (rejected data), #345 (deletions), #337 (soft clipping), and #338 (insertions).

Other changes:

• #344 replace R coverage maps with Python version
• #343 several improvements to how the monitor handles cancelled runs and purged results
• #340 consensus for two references drifted past each other

For the full list, see the milestone.

G2P Improvements

There were a couple of improvements to the G2P: #318 to stop reporting G2P sequences with low count, and #317 to convert "ambiguous" from an error to a comment.
Other significant changes:

• #280 Improve handling of single bar code
• #299 Coverage drop at ends
• #336 Add new references for ERCC SRM control sequences enhancement

See the milestone for the full list.

BaseSpace patches

Fix a crash in the BaseSpace version when nothing maps to one of the samples.

Also fix a couple of matplotlib warnings in the BaseSpace version:

• #323 more than 20 figures
• #324 building font cache

There weren't any changes to the Kive version.

BaseSpace

Write a new driver to execute the pipeline on Illumina's BaseSpace platform, issue #204.

• #316 add a new NS5a project
• #311 V3LOOP drifting to HCV

For the full list of issues, see the milestone.

Prune by distance from seed

The main issues in this release are:

• #290 Prune by distance from seed reference
• #295, #301, #303, #304, and #307 several G2P bugs
• #300 add G2P summary
• #305 remove minimum reads for V3LOOP

For the full list of issues, see the milestone.

Remove key position 348 from RT

The main issue for this release is #283 to remove key position 348 from RT. However, that required several changes to support reprocessing old runs with a new version of the pipeline. That was covered in issue #282, along with processing multiple runs in parallel.

Multiple runs per day

Issue #233 supports multiple runs per day by adding a suffix to the run name.