polish alignment kernel options

[mmolari]

This PR should contain the following changes:

• remove minimap2-cli option for the alignment kernel. The reason is that this should be redundant, given that we already ported the minimap library
• improve the external call to mmseqs2 and parsing of the output
• add an initial check for the availability of the mmseqs command in path
• fix error with mmseqs intervals

[mmolari]

running target/release/pangraph build -k mmseqs data/mpox.fa with mmseqs version 17.b804f currently results into this error:

Error: 
   0: When traversing guide tree
   1: When merging graphs
   2: During self-merge iteration 0
   3: During reweave
   4: When splitting block 1
   5: When extracting intervals for block 1
   6: When performing interval sanity checks
   7: Last interval does not end at the block length. Interval: [190088, 197210), block length: 197209. This is an internal error. Please report it to developers.

Location:
   packages/pangraph/src/pangraph/pangraph_interval.rs:60

I need to investigate further, probably just a matter of 1-based vs 0-based indexing.

Edit: indeed, according to the documentation while mmseqs standard output see uses 0-based indexing, the use of --format-output results in 1-based indexing. This was not a problem in julia (1-based indexing). It was easily fixed by correct indexing conversion.

[mmolari]

Now error messages are more informative:

If mmseqs is not available in path:

Error: 
   0: When performing preliminary checks before building the pangraph.
   1: Executing `mmseqs --help` results in the following error:
      No such file or directory (os error 2)
      Please make sure that `mmseqs` is installed and available in PATH.

Location:
   packages/pangraph/src/commands/build/build_run.rs:23

If mmseqs command returns an error:

Error: 
   0: When traversing guide tree
   1: When merging graphs
   2: During self-merge iteration 0
   3: mmseqs command exit status: 1
      failed with stderr:
      Unrecognized parameter "--threds". Did you mean "--threads" (Threads)?

Location:
   packages/pangraph/src/align/mmseqs/align_with_mmseqs.rs:57