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Clojure only.

Various sequence aligners by means of low level hackery...

Various sequence aligners by means of low level hackery...

```
(align s1
s2
&
{:keys [kind submat gap match mmatch decode keep-scmat]
:or {kind :global gap -2 decode true keep-scmat false}})
```

Align s1 and s2 (strings) in the manner defined by kind:

:global - Standard NW global alignment :ends-gap-free - global aln without gaps on ends (prefix/suffix aln) :local - Standard SW alignment

submat is a substitution map (matrix) giving a score for a character pair. This namespace provides nt4submat which encodes a 'standard' ATGCxATGC substitution matrix.

match is a score for the case when characters match (they are =) mmatch is a penalty score for the case when characters do not match

submat and match/mmmatch are mutually exclusive

gap is a penalty score for indels (characters match a gap)

keep-scmat is a boolean for whether to return the scoring matrix (true) or not (false)

Returns the traceback path of best alignment as a vector of triples: [dir score [i j]], where dir is the direction to get this point of path (:d -> diagonal, :u -> up, :l -> left), score is the score at this point, and [i j] is the index pair for s1 and s2 of this point (i for s1, j for s2) 0-based.

If decode is true (default), tb is returned as the pair of aligned strings (with gaps if needed)

If keep-scmat is true, returns a vector [tb scmat] otherwise returns just tb, tb the traceback.

Align s1 and s2 (strings) in the manner defined by kind: :global - Standard NW global alignment :ends-gap-free - global aln without gaps on ends (prefix/suffix aln) :local - Standard SW alignment submat is a substitution map (matrix) giving a score for a character pair. This namespace provides nt4submat which encodes a 'standard' ATGCxATGC substitution matrix. match is a score for the case when characters match (they are =) mmatch is a penalty score for the case when characters do not match submat and match/mmmatch are mutually exclusive gap is a penalty score for indels (characters match a gap) keep-scmat is a boolean for whether to return the scoring matrix (true) or not (false) Returns the traceback path of best alignment as a vector of triples: [dir score [i j]], where dir is the direction to get this point of path (:d -> diagonal, :u -> up, :l -> left), score is the score at this point, and [i j] is the index pair for s1 and s2 of this point (i for s1, j for s2) 0-based. If decode is true (default), tb is returned as the pair of aligned strings (with gaps if needed) If keep-scmat is true, returns a vector [tb scmat] otherwise returns just tb, tb the traceback.

`(decode-trace-back s1 s2 tbk)`

`(deep-aget hint array idx)`

`(deep-aget hint array idx & idxs)`

`(deep-aset hint array & idxsv)`

`(do-col scmat col e & body)`

`(do-row scmat row e & body)`

```
(hirsch-align sx
sy
&
{:keys [kind submat gap match mmatch with-score? score-only?]
:or {kind :global gap -2 with-score? true}})
```

`(hirsch-align-recur sx sy & {:keys [kind submat gap match mmatch]})`

`(lcsubseq s1 s2)`

`(lcsubstg s1 s2)`

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