1.2.0

• Now supports an optional --coverage argument to produce abundance profiles based on coverage information instead of abundance
• Improved documentation
• Fix for #64

1.1.2

• Fix #59
• Switch to pipenv for development
• Small changes to documentation

Bug Fixes

This patch release contains bug fixes and documentation improvements

• --n_genomes works again with the --ncbi option
• the examples in the documentation should be more clear

Minor Release

This release introduces the possibility to use --n_genomes/-u with --genomes

In other words, you can now generate reads from a random subset of a multifasta file 🎉

Patch Release

This is a minor bugfix release:

• Fix python2 compatibility error for downloading genomes from the ncbi ( #45 )

• Fix python2 error handling when a genome fails to download

• Fix crash for when a genome is shorter than the template length ( #45 ):
  now uses a simpler error model and allow negative insert size. Will crash (rightfully) is a genome is shorter than the read length

Stable Release

This is the first stable release if InSilicoSeq 🎉

Changes:

• --model is now case insensitive
• --kingdomis no longer limited to a single kingdom and now accepts a combination of bacteria, viruses and archaea

Bugfixes:

• fixes a lot of error handling that were python3 specific and made the python2 version crash

Beta Release

Bugfixes:

• iss generate now saves the abundance in a file ( #36 )
• iss generate now prints a warning if a user try to use an error model in --mode basic ( #38 )
• fixes a bug that crashed the app with the default number of reads ( #40 )
• fixes a bug that sometimes prevented the software to cleanup properly ( #41 )

Thanks to @jhayer for a help! 🚀

Beta Version

This release brings bug fixes and small enhancements.

Changes:

• deprecation of the 1D KDE. 2 Dimensional KDE is now the only other error model available together with the basic one
• the option --model has been renamed mode and is KDE by default (see #30 )
• the option --model_filehas been renamed model and uses the HiSeq error model by default
• the --n_reads option now allows suffixes 'G', 'M' and 'K' both in lower and uppercase. (see #29 )
• iss --version and iss -v now print the version number and exit. (see #27 )

Bugfixes:

• the temporary files are now cleanup up if the user interrupts iss generate ( see #31 )
• the empty genomes are now correctly skipped if you use the --ncbi option (see #32 )
• the --gc_bias options is functioning again ( see #33 )
• the NovaSeq and HiSeq error models are now really usable (see #34 )

0.7.0 Beta Release

This releases mainly adds error models.

Changes:

• added a NovaSeq error model
• updated MiSeq and HiSeq error models
• counting bam records is now way faster

Bug fixes:

• fixed a bug that affected reads mapped against the reverse complement
• changed the matrix transposition method leading to smaller file size for the error models

0.6.0 Beta Release

This release includes changes to the iss model module.

Changes:

• iss model now constructs its statistical model on 1 million reads instead of the entire bam file
• no loss of base quality accuracy could be detected
• greatly speeds up model generation (~20 minutes against ~100 minutes before)
• reduces memory usage