Multiple genotypes RC4

Another tweak to the logging settings.

For a full list of issues, see the milestone.

Multiple genotypes RC3

Bug fix for #270.

For a full list of issues, see the milestone.

Multiple genotypes RC2

Minor change to the logging settings.

For a full list of issues, see the milestone.

Multiple genotypes

The main feature is #160 to use separate references for each HCV genotype. Other important issues:

• #228 problems with G2P results when compared with 454 data
• #264 lower coverage after adding multiple genotypes

For a full list of issues, see the milestone.

Stand-alone preview

The main feature in this release is a stand-alone version of the pipeline, packaged to run on Windows (issue #234). We also report multiple genotypes of HCV (issue #160), and removed our dependencies on Ruby and samtools.

Gap penalty adjustment

The main fix is for #189, increasing gap open penalty. We also corrected the HLA-B coordinate reference to use the proper reading frame.

For the full list of changes, see the milestone.

Bug fix

Added wrong commit to v6.7.2

Cleaning up intermediate files from older runs

Emergency patch for release 6.7. Fixes #185. MISEQ_MONITOR.py checks if the run being processed is one of the latest X runs (see nruns_to_keep parameter in settings.py). If yes, then all intermediate files are retained after processing. If no, then a number of large intermediate files are removed from the run folder after processing.

Rejecting low-quality tile cycles

The main changes for this release:

• #162 Reject reads with poor quality control measurements
• #173, #176, #177, and #178 change project definitions

For the full list of changes, see the milestone.

HCV genotypes

Map to many HCV genotype seeds, add mini projects, and fix several output problems with blanks and dashes. See the 6.6 milestone for a complete list of issues.