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Option for vg call to select reference paths by sample name #4031

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merged 1 commit into from
Jul 26, 2023

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Changelog Entry

To be copied to the draft changelog by merger:

  • -S option added to vg call to select reference paths by sample name. This is more convenient as it allows, ex -S GRCh38 to be used in place of -p GRCh38#0#chr1 -p GRCh38#0#chr2 ... Such selection is necessary when the graph has more than one reference sample and vg call will now refuse to handle graphs with multiple reference samples unless paths are selected with -S or -p.

Description

This is critical for calling on the v1.1 HPRC graphs, which contain both GRCh38 and CHM13 as reference samples. Whereas running call without any path selection worked fine on the v1.0 graphs (which had a single reference sample), it makes a big mess on the newer graphs as it calls on both references at once...

@glennhickey glennhickey merged commit 942c2ea into master Jul 26, 2023
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