Refactor handling of virtual contigs#489
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alimanfoo merged 10 commits intomalariagen:masterfrom Dec 20, 2023
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## master #489 +/- ##
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+ Coverage 98.42% 98.49% +0.07%
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Files 30 30
Lines 2408 2520 +112
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+ Hits 2370 2482 +112
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Towards #366, refactor handling of virtual contigs.
The main benefit here is that it allows testing using simulated data.
Also configuration of virtual contigs is more flexible, a virtual contig can be made of any number and combination of reference genome contigs.
Also here a
haplotype_sites()function is surfaced in the public API - it's required internally within G123 but moving to public API as could be generally useful.