; pass to ngalign_app as the 'run' parameter, configures all of the CNgAligner stuff
; some values, like 'blastdb' path need to still be on the command-line.
; anything like filter and score on command-line override whatever is in here

[query]
; NgAligner.SetQuery()
type=seqidlist
; common type values are 
;   seqidlist
;   blastdb
; uncommon values are
;   seqloclist (id:start-stop) for bounded alignments
;   fasta (will load fasta file into Scope, and use fasta ids as seqidlist)
;   splitseqidlist  : For alignment Delta-seqs by their parts, like phase-1 clones, 
;   splitseqloclist :  then re-assembling the final alignment. 

[subject]
; NgAligner.SetTarget()
type=blastdb
; see query


[filters]
; NgAligner.AddFilter()
; there must be a 'names'
names = perfect good ok terrible
; which lists the other values to pull filters from
perfect = 	" pct_identity_ungap >= 99.0 AND pct_coverage >= 99.0 AND common_component = 1 "
good = 		" pct_identity_ungap >= 99.0 AND pct_coverage >= 99.0 "
ok = 		" pct_identity_ungap >= 95.0 AND pct_coverage >= 95.0 " 
terrible = 	" pct_identity_ungap >= 80.0 AND pct_coverage >= 25.0 "
; the names 'perfect', 'ok', etc are not what is important, i
; just that 'names' points to valid filter strings
;
; The filters will be uses in 'names' order

[scorers]
; NgAligner.AddScorer()
names = blast pctident pctcov comcomp expansion 
; which scorer objects to use
; common values
;   blast : all the normal scores 'blast' puts on an alignment
;   pctident : puts all three percent ident scores on alignments
;   pctcov : normal percent coverage, of the query side 
; uncommon values  
;   comcomp : for determining if the delta-seqs the query and target ranges aligned are identical 
;   expansion : full range alignment bounds (with gaps and stuff) divided by ungapped bases in alignment
;   weighted : calculated best_placements 'weighted_identity' score
;   clip : calculates common scores, but only taking into account the region of the i
;        : query sequence marked 'high_quality' by a region feature on the query sequence record

sw_cvg = 0.04 
; provides a best_placement sw_cvg value, used by 'weighted' and 'clip', defaults to 0.04
  

[aligners]
; NgAligner.AddAligner()
names = blast merge 
; which alignment steps to use, in order. These words are used as
;  [section] names below, where their section will contain more detailed config for the aligner

; the names 'blast' or 'merge' are not signifigant, that is determined by the 'type' 
;  value in the [section]

; example, used alignment configs here
[blast]
type = blast
threshold = 0
params = " -word_size 32 -evalue 0.0001 -soft_masking true  -best_hit_overhang 0.1 -best_hit_score_edge 0.1 " 

[merge]
type = merge
threshold = 0
mode = tree

; unused examples
[dummy]
type = blast
; common type values
;   blast : CLocalBlast basically
;   merge : either CAlignCleanup or CTreeMerger
; uncommon type values
;   remote_blast : CRemoteBlast
;   inversion : creates disc-seg alignments where two alignment of opposite strand seem to belong together
;   split : chunks sequences into their delta-seq parts, see 'splitseqidlist' from query/target
;   file : reads in a (seq-align,seq-align-set,seq-annot) asn text file, forwards them through the process
;        : like debugging later steps but starting with a constant blast alignment file

threshold = 0
; all aligners have a 'threshold' value
; if a query sequence has alignments better than (>, not >=) in the filter scores, this alignment step
; will pass on that query. Usefull for skipping computationally expensive steps that aren't needed
; like when 'banded' was still used...

; type-specific parameters

; type = blast
params = "  -word_size 32 -evalue 0.0001 -soft_masking true "
; blastn command line string to configure CLocalBlast
filter = windowmasker 
; blastdb filter string (or backwards integer) 

; type = merge
mode = tree 
;  'tree' for tree merger, 'cleanup' for CAlignCleanup
; an unused 'clip' value could be found here, has part of configuring tree merger's scoring
;  but its not usable as-is.

; type = remote_blast
; none. the remote database like 'nr' is provided through the target blastdb value

; type = inversion
;  none
; type = split
;  none
 
; type = file
filename = /my/path/to/align/text/file.asnt
; file it reads in and outputs to later stages