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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 15:36:39 +01:00
parent 402d54cb62
commit 2163db94d0
4 changed files with 32 additions and 24 deletions
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34
pkg/obialign/pairedendalign.go
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@@ -51,17 +51,17 @@ func __get_matrix_from__(matrix *[]int, lenA, a, b int) (int, int, int) {
}
func __pairing_score_pe_align__(baseA, qualA, baseB, qualB byte) int {
part_match := __nuc_part_match__[baseA&31][baseB&31]
part_match := _NucPartMatch[baseA&31][baseB&31]
// log.Printf("id : %f A : %s %d B : %s %d\n", part_match, string(baseA), qualA, string(baseB), qualB)
switch {
case part_match == 1:
// log.Printf("match\n")
return __nuc_score_part_match_match__[qualA][qualB]
return _NucScorePartMatchMatch[qualA][qualB]
case part_match == 0:
return __nuc_score_part_match_mismatch__[qualA][qualB]
return _NucScorePartMatchMismatch[qualA][qualB]
default:
return int(part_match*float64(__nuc_score_part_match_match__[qualA][qualB]) +
(1-part_match)*float64(__nuc_score_part_match_mismatch__[qualA][qualB]) + 0.5)
return int(part_match*float64(_NucScorePartMatchMatch[qualA][qualB]) +
(1-part_match)*float64(_NucScorePartMatchMismatch[qualA][qualB]) + 0.5)
}
}
@@ -73,7 +73,7 @@ func __fill_matrix_pe_left_align__(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gap = gap * __nuc_score_part_match_mismatch__[40][40]
gap = gap * _NucScorePartMatchMismatch[40][40]
needed := (la + 1) * (lb + 1)
@@ -144,7 +144,7 @@ func __fill_matrix_pe_right_align__(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gap = gap * __nuc_score_part_match_mismatch__[40][40]
gap = gap * _NucScorePartMatchMismatch[40][40]
needed := (la + 1) * (lb + 1)
@@ -215,9 +215,9 @@ func __fill_matrix_pe_right_align__(seqA, qualA, seqB, qualB []byte, gap int,
func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
if !__initialized_dna_score__ {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix()
_InitDNAScoreMatrix()
}
if arena.pointer == nil {
@@ -229,7 +229,7 @@ func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (in
&arena.pointer.score_matrix,
&arena.pointer.path_matrix)
arena.pointer.path = __backtracking__(arena.pointer.path_matrix,
arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
seqA.Length(), seqB.Length(),
&arena.pointer.path)
@@ -238,9 +238,9 @@ func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (in
func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
if !__initialized_dna_score__ {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix()
_InitDNAScoreMatrix()
}
if arena.pointer == nil {
@@ -252,7 +252,7 @@ func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (i
&arena.pointer.score_matrix,
&arena.pointer.path_matrix)
arena.pointer.path = __backtracking__(arena.pointer.path_matrix,
arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
seqA.Length(), seqB.Length(),
&arena.pointer.path)
@@ -269,9 +269,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
var raw_seqB, qual_seqB []byte
var extra5, extra3 int
if !__initialized_dna_score__ {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix()
_InitDNAScoreMatrix()
}
index := obikmer.Index4mer(seqA,
@@ -323,7 +323,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
&arena.pointer.path_matrix)
}
arena.pointer.path = __backtracking__(arena.pointer.path_matrix,
arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
len(raw_seqA), len(raw_seqB),
&arena.pointer.path)
@@ -349,7 +349,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
score = 0
for i, qualA := range qual_seqA {
qualB := qual_seqB[i]
score += __nuc_score_part_match_match__[qualA][qualB]
score += _NucScorePartMatchMatch[qualA][qualB]
}
arena.pointer.path = arena.pointer.path[:0]
arena.pointer.path = append(arena.pointer.path, 0, part_len)