Feat/nested variation ref selection #19
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- Add nested_mode flag to config (defaults to true) - Build reference preference order from sample prefixes and GFA order - Select best reference per flubble based on preference order - Output single unified VCF with each variant reported once - All samples included in VCF header This mode allows prioritizing references so each variant is called against the most preferred available reference, reducing redundancy in VCF output.
- Change reference group validator from Xor to AtMostOne - When no references specified, uses all paths in GFA order - Allows running: povu call -i graph.gfa --stdout - Maintains backward compatibility with explicit reference selection
- Collect which references are actually used during VCF generation - Add init_vcfs_nested() that only writes contig lines for used refs - Buffer VCF records in nested mode to determine used refs first - Ensures VCF header only contains contigs that appear in the data
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This allows sets the default behavior of povu to write all sites, choosing the appropriate reference for them based on a priority order of the paths in the graph, which is given by a prefix list, which can be written on the command line, given by file. And if none is given, the order in the GFA is taken. if only one or a subset of the of the paths prefixes as given then we use that to to see the order and then fill the rest in with those in order in the respective order from the GFA file.