4Pipe4-1.7.1

This point release adds some documentation updates to 4Pipe4.
No code was changed from 1.7.0.

4Pipe4-1.7.0

This new release adds the option to use illumina data on 4Pipe4.
However, keep in mind that 4Pipe4 was designed for 454 data, and although everything should run using illumina data, it's performance was not nearly was tested as the performance with 454 data.
Therefore, the software is usable, but YMMV with the default values for illumina data. In fact, any feedback with this sort of data is very appreciated.

4Pipe4-1.6.0

This release has dropped a SNP filtering step.
This means that SNP detection routines performance has effectively doubled.
It also brings better PEP8 conformance.
Furthermore, some dead links in the helper scripts were corrected.

4Pipe4-1.5.1

This release has dropped the use of git packages and now uses only stable packages.
This meant requiring python >= 3.4.x for the latest pysam release, which relies on cython 0.22, which requires python 3.4.

No longer relies on buggy CAF output

Version 1.5 of 4Pipe4.

• Dropped the sff_extract dependency (and therefore python2 dependencies)
• Now requires pysam
• The helper scripts were greatly improved
• A lot of bugfixes

v1.3

This release will now write all the output files of 4Pipe4 into the basedir.
This will break compatibility with older versions.
If you want to use 4Pipe4 v1.3 and above with any of your older data, you should copy (or link) the file basename/_basename__assembly/_basename__d_results/_basename__out.short.tcs to the basedir.