Changed

the 7mer context for r9 to a 5mer context
- some data showed significant signals near a mutation that are within a 7mer context, but not a 5mer context - hard to say if from mutation or not (no proof). Therefore, stick to the number of nucleotides measured together depending on the pore-type.
MeanDiffAvgStdDev plots are now called MeDAS, meaning Mean Distance Average Standard-deviation
- MeDAS plots showing the coverage
- plots are now created using the magniplot.py
- before: created with magnipore.py
change part of logger file name created by the subscript nanocherlock.py from "magnipore" to "nanosherlock"
gzip will now overwrite already existing output files
summary output
- typo fixes
- less redundant text
- more information about number of positions
replaced minimap2 with winnowmap
changed winnowmap parameters to the default values used by the ont_aligner toolchain from Oxford Nanopore Technologies

Added

different ranges for the classification of a significant signal into mutation or potential modification depending on the pore type
- r9: 5mer context
- r10: 9mer context
magnifilter.py: a script to filter the given .magnipore output file for a given coverage threshold
magnicheck.py: a script to check if magnipore found the positions in a context of given validated ground truth positions
multiprocessing of magnipore model comparisons
Error for empty f5c file
- 027: f5c eventalign file is empty