Nanoraw

- More flexible multithreading
- including more intuitive --processes argument that defines global number of processes
- Better error checking
- Several bug fixes
- Convenience --recursive option for new sub-directory structure

- Added pA normalization
- Added sliding window for clustering
- Better strand handling for plotting
- Bug fixes

- Two major bug fixes to last release
- OBO error in ambiguous indel correction code (homo-polymer correction code)
- error handling code
- removed rpy2 as a requirement; simply a recommendation for plotting functions now
- this was the most cumbersome dependency
- for users that don't need plotting functionality it is easier not to install rpy2

- Wiggle output for statistics, signal level, coverage and more
- Better homo-polymer correction (as well as all ambiguous indels)
- Support for mapping with BWA-MEM (and easier incorporation of any mapper that outputs SAM)
- Batched alignment calls (Should greatly accelerate alignment for larger genomes)
- Separated alignment and re-squiggle code into separate processes linked via queues
- Several code optimizations
- Bug fixes

Preprint manuscript code version.

Major change was adding option for Fisher's Method.

- Added Mann-Whitney U-test to identify DNA Modifications
- pA and raw (no norm) normalization added
- observations per base quantile filter added
- new visualizations
- multiple testing corrections
- signal based clustering
- example commands added in /nanoraw/tests/shell_test.sh
- bug fixes