0.5.1 Beta Release

This is a bugfix release

Minor changes:

• Fixed installation problem

0.5.0 Beta Release

This release adds multiprocessing support for the read generation module 🎉

Major changes:

• Multiprocessing! iss generate now uses 2 cpus as a default
• change the number of cpus with --cpus or -p

Minor changes:

• somewhat updated documentation

0.4.1 - Beta Release

This is a bug fix release.

Bug Fixes:

• The deletion code no longer sometimes causes an IndexError ( #21 )
• Trying to introduce sequencing errors on ambiguous bases no longer crashes the software ( #20 )

Beta Release

Major changes:

• The main error model switched from a simple Kernel Density Estimation to a two-dimensional Kernel Density Estimation. The new model is better at estimating the mean sequence quality and produces more realistic sequences overall
• The insert size of the generated pairs is no longer fixed but follows a more realistic distribution
• added a --gc_bias option to naively discard some sequences that fall outside a normal range of GC content.

Bug fixes:

• fixed a bug that would affect the substitution rate for T, G and Cs

Beta Release

Changes:

• New --abundance parameter. InSilicoSeq doesn't require an abundance file anymore and can model an abundance distribution
• New --ncbi parameter. You don't necessarily need input genome(s) either, they can be randomly downloaded from ncbi genomes!

Bug Fixes:

• the indel generation code now skips Ns instead of failing

Rollback prebuilt error models

This release is basically 0.2.1 without the 3 new error models

Beta release

Changes:

• 3 (better) error models
• Updated documentation
• New code of conduct and Contributing guidelines
• Now on Pypi

2nd alpha release

Changes:

• two pre-computed error models available: HiSeq2500 and MiSeq
• updated docstrings, comments and documentation
• backwards compatibility with python 2.7

first alpha release

First ever release of InSilicoSeq 🚀 🎉

Early alpha release.

• two subcommands, iss model and iss generate
• three errors models: kde, cdf (might be deprecated) and basic
• two install methods, pip and docker
• probably lots of bugs