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Annotations for community definitions #27

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cerebis opened this issue Jan 17, 2024 · 1 comment
Open

Annotations for community definitions #27

cerebis opened this issue Jan 17, 2024 · 1 comment

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@cerebis
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cerebis commented Jan 17, 2024

Currently, many simulation options are an all-or-nothing operation that affect the entire community.

Adding these are annotations within the community definition would provide valuable fine-grained control.

Example

Simulations that involve complete non-circular or fragmentary draft genomes should be simulated as linear segments -- meaning their contacts will not include features due to circular topology. Currently, this is achieved with the runtime option --linear, which is then applied to all reference sequences in the community.

Instead, we could have an optional detail within the community flagging those sequences (or cells) are are linear.

This annotation style could be used for other simulation details, including interaction rates.

cerebis added a commit that referenced this issue Jan 30, 2024
- addressed oversight in object identity within Community
- added TOML-format profile definition
- fixed normalisation error introduced with addition support for fragmented genomes
- better error reporting reading profiles
- minor fix of version stamp
@cerebis
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cerebis commented Jan 30, 2024

Review #30 to see changes that allow a greater degree of control.

@cerebis cerebis mentioned this issue Jan 30, 2024
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