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cerebis / sim3C

Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
GNU General Public License v3.0
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Annotations for community definitions #27

Open cerebis opened 8 months ago

cerebis commented 8 months ago

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 commented 8 months ago

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