Compatibility with bpipe 0.9.12

• Fix issue with empty params initialising to booleans
• Setup references: update gffread URL to https

MINTIE v0.4.2

Reference update

MINTIE v0.4.1

Release to trigger bioconda rebuild (0.4.0 failed due to CircleCI issue).

MINTIE v0.4.0

Support for single-end data.

MINTIE v0.3.9

Added wrapper script.

MINTIE v0.3.8

Fix for setting up references

MINTIE v0.3.7

Portability fixes

MINTIE v0.3.6

• Removed legacy viz functions
• filter_fasta.py optimisation

MINTIE v0.3.5

• Added 40bp sequence output for each variant's position (20bp flanking either side of each position)
• INDEL simulation now allows setting constant size
• Improved retained intron detection
• Minor fixes and improvements

MINTIE v0.3.0

• Numerous bug fixes
• Compatibility for salmon v1+
• Added intragenic rearrangement (IGR) variant type
• Motif checking leniency (+ motifs are now returned in an output column)
• Variant sizes have been fixed for numerous splice variants and TSVs
• Check kmer params when running assembly
• Tweaks to default config parameters