I have a graph that I created and indexed using:
vg construct -v vars -r ref -a >graph.vg vg index -x graph.xg graph.vg vg index -G graph.gbwt -v vars graph.vg
The VCF used for construction has phased genotypes for all 7 chromosomes, so I would expect 14 haplotype threads. However vg paths reveals many more than that, 945.
vg paths -g graph.gbwt -x graph.xg -E _thread_ZI284_NC_004353.4_0_1 127100 _thread_ZI284_NC_004353.4_1_1 127104 _thread_ZI284_NC_004354.4_0_0 932781 _thread_ZI284_NC_004354.4_1_0 932778 _thread_ZI284_NC_004354.4_0_1 627525 _thread_ZI284_NC_004354.4_1_1 627553 _thread_ZI284_NC_004354.4_0_2 992875 _thread_ZI284_NC_004354.4_1_2 992884 _thread_ZI284_NC_004354.4_0_3 113038 _thread_ZI284_NC_004354.4_1_3 113036 _thread_ZI284_NC_004354.4_0_4 319932 _thread_ZI284_NC_004354.4_1_4 319953 _thread_ZI284_NC_004354.4_0_5 102680 _thread_ZI284_NC_004354.4_1_5 102686 _thread_ZI284_NC_004354.4_0_6 122150 _thread_ZI284_NC_004354.4_1_6 122160 _thread_ZI284_NC_004354.4_0_7 41509 _thread_ZI284_NC_004354.4_1_7 41514 _thread_ZI284_NC_004354.4_0_8 62633 _thread_ZI284_NC_004354.4_1_8 62637 _thread_ZI284_NC_004354.4_1_9 422021 _thread_ZI284_NC_004354.4_0_9 1177293 ...
I see there are two 'main' threads:
What are the other threads? And what does the 'x' represent? Are they just parts of the collective thread?