probe match shall support more types of "weak matches"

[westram]

Types of weak matches currently supported by PT-Server:

• mismatches
• N-mismatches

It should also support these types:

1. IUPAC codes in 'Target string'
2. insertions
3. deletions

Needed additional parameters:

• max. number of insertions and deletions allowed
• mismatch-penalty for inserts + deletes (each using 2 penalties, e.g.: one for initial insert, another for extending that insert)
• mismatch-penalty for IUPAC-matches?
  • maybe specify a general weight-factor (for IUPAC and N-matches),
  • calculate some kind of weighted mismatch from
    • the probabilities of the specific bases (defined by IUPAC/N) and
    • their transition/transversion penalties and
  • add weight-factor * mismatch-weight to current (weighted) mismatch value. That would allow to either ignore IUPAC-mismatches (by setting the weight to zero) or to count/weight them as mismatching.

Prefix (PT) traversal:

• needs to carry much more state-information, e.g. number of inserts/deletes performed (absolute + extends),
• has to be able to properly undo state-modifications (performed during descent) while ascending and
• should descent into all additional prefixes that get possible by inserting/deleting bases.

While traversing PT, matches get collected and need to get categorized into

• impossible matches,
• definite matches and
• possible matches (which need further inspection).

Reasons why a hit may be classified as possible match:

• target string is longer than PT-depth (⇒ reaches cut-off at tips of PT)
• whenever any other cut-off in PT is reached (e.g. 'N' or IUPAC-code occurred in input sequence data)

Possible matches need to inspect the actual sequence data and evaluate the "rest" of the target string against it.

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Related: #746, #747
Superseeds: #543