0.5

Version 0.5:

• 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

0.4.2

Version 0.4.2

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

0.4.1

Version 0.4.1

• 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

0.4

Version 0.4:

• 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

0.3.1

Preprint manuscript code version.

Major change was adding option for Fisher's Method.

0.3

Version 0.3

• 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

0.2

Version 0.2

• Overhaul of plotting subcommands to pivot on type of region to plot
• Added plotting of the genome-guided read correction process
• Support for correction and plotting of complement reads
• Select deepest coverage regions at k-mer of interest (instead of randomly selected)
• Changed overplotting default to downsample (via randomly selected reads) to the overplotting threshold

0.1

First version up on pip.