Long read giraffe parameter smoothening

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• vg giraffe --max-chains-per-tree works as documented (bugfix)
• vg giraffe --min-chains is now --target-alignment-attempts and has better documentation
• Minor vg giraffe chaining mode speedup

Description

First item on the list is what I mentioned in Slack about us accidentally passing --max-alignments in the find_best_chains() function call where we meant --max-chains-per-tree. Second is also something we talked about in Slack about a parameter that I didn't understand and messed with incorrectly. Third is that, since it's not necessary, we no longer pass gap_open & gap_extend into chaining (we now score transitions using Minimap2-style logged-gap scoring), and chain_items_dp() now only calculates the max DP cell if show_work is turned on since we don't really need it downstream and why not save ourselves yet another pass through the anchors. The only functionality change is to the sr-chaining preset.