OMSim v1.2.2

Changes:

• Add (min|max)_num_mol settings to control number of molecules
  • Check the wiki and new examples to see how these work
• Fix original molecule ID in output, it used to be always 1, now it makes a bit more sense, maybe.
• Fix bug when empty BNX is generated
• Sort nicks per molecule, to ensure they are from low to high

OMSim v1.2.0

Note: Paths in the simulation XML are now relative to the working directory, as opposed to the XML file location in earlier versions.

Changes:

• Fixed bug reading all input paths relative to XML file instead of current directory. (#17)
• Take stretch factor into account when determining number of molecules
• Compute pixels per scan straight from scan length and bases per pixel
• Fix coverage off-by-one error
• Add script to download public BNX data from NCBI

OMSim v1.1.10

• Add fixed_stretch_factor_estimate setting
  • this setting is illustrated in example/Fixed-SF-Estimate
• Fixed bug setting directory for multiple simulations incorrectly. #15

OMSim v1.1.9

FIx #14

OMSim v1.1.8

Fix #13

v1.1.7

• Fix stretch_mol_sd setting

OMSim v1.1.6

• Fix BED file output for reversed molecules
• Add always_forward simulation option, set this to 1 to only simulate molecules in the same direction as the reference sequence
• Add link to publication to readme

OMSim v1.1.4

• Change sigmoid behaviour such that S(x) always returns 0 if factor (fragile_factor or label_factor) is 0
• Updated OMSim's internal version number, this was still at "v1.1.0" in the previous releases.
  OMSim should now correctly print "Version: v1.1.4"

OMSim v1.1.2

• add multiple examples
  1. Irys: for default settings for the Irys platform
  2. Saphyr: for default settings for the Saphyr platform
  3. Noiseless: an annotated example of how all noise sources can be disabled
• minor changes and fixes to support the Noiseless example, in particular some potential ZeroDivisionError are fixed
• adds two boolean settings do_not_merge_bnx and bed_file, to control the output file behaviour

OMSim v1.1.1

Add multi-channel bnx support