Fix chunk extraction and subsequent GBWT generation

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg chunk and vg find now generate subpaths with subrange metadata when cutting up paths.
• vg gbwt will accept subranges on fragment 0 and discard the fragment number.

Description

This should let you do:

wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.chroms/chr20.d9.vg
vg snarls -t8 -a chr20.d9.vg > chr20.d9.snarls # get snarls
vg chunk -x chr20.d9.vg -p CHM13#chr20:5000-15000 --snarls chr20.d9.snarls > chr20_10k.vg # get the subgraph
vg gbwt -E -x chr20_10k.vg -o chr20_10k.gbwt

But it changes a lot of how chunk extraction on reference paths names things, so it might break a bunch of CLI tests. And it needs some unit tests to make sure that subpath start offsets are accurately computed.