More Realistic Simulation

What's new in 0.17.1

New Features

• Enabled simulating data with no two mutations too close (controlled by --min-mut-gap).
• Changed behavior of the mutation rate simulator so that each base has the same paired and unpaired mutation rates in every cluster, which is more realistic than the previous behavior of entirely different mutation rates in every cluster.
• Added feature where the Illumina universal adapter (AGATCGGAAGAGC) is appended automatically to any insert that is shorter than the read length, to make the simulation mimic Illumina sequencers more realistically.
• Updated the directory structure of the simulation outputs to avoid possible name conflicts.
• Added subcommand seismic +sim params to simulate all parameters in one step.
• Added option --fq-gzip/--fq-text simulate FASTQ files with or without gzip compression.

Bug Fixes

• Fixed bug in seismic fold where a temporary CT file would be written to the output directory.

Full Changelog: v0.17.0...v0.17.1