Update NOVOPlasty4.3.5.pl

ndierckx · web-flow · commit 12ea0cb1bfa5 · 2024-02-04T22:10:53.000+09:00
diff --git a/NOVOPlasty4.3.5.pl b/NOVOPlasty4.3.5.pl
@@ -10041,13 +10041,14 @@ sub align_hp
                     my @IUPAC = IUPAC($nucs{"A"},$nucs{"C"},$nucs{"T"},$nucs{"G"},$hp);
                     if ($IUPAC[0] eq "A" || $IUPAC[0] eq "C" || $IUPAC[0] eq "T" || $IUPAC[0] eq "G")
                     {
+                        $best_extension = $best_extension.$IUPAC[0]; 
                     }
                     else
                     {
+                        $best_extension = $best_extension."N"; 
                         $SNP++;
                     }
                     $allele_percentage{$l} = $nucs{"A"}."+".$nucs{"C"}."+".$nucs{"T"}."+".$nucs{"G"};
-                    $best_extension = $best_extension.$IUPAC[0]; 
                 }
                 elsif ((($heteroplasmy ne "" && $l < $pos_SNP4+10) || $heteroplasmy eq "") && $SNP eq "4" && ($pos_SNP ne 0 || ($pos_SNP4 > $pos_SNP+12) || ($extensions_before eq "yes" && $l > 12)))
                 {
@@ -18432,13 +18433,14 @@ sub align_hp
                     my @IUPAC = IUPAC($A,$C,$T,$G);
                     if ($IUPAC[0] eq "A" || $IUPAC[0] eq "C" || $IUPAC[0] eq "T" || $IUPAC[0] eq "G")
                     {
+                        $best_extension = $best_extension.$IUPAC[0]; 
                     }
                     else
                     {
                         $SNP++;
+                        $best_extension = $best_extension."N"; 
                     }
-                    $allele_percentage_back{$l} = $A."+".$C."+".$T."+".$G;
-                    $best_extension = $best_extension.$IUPAC[0]; 
+                    $allele_percentage_back{$l} = $A."+".$C."+".$T."+".$G;                   
                 }
                 elsif ((($heteroplasmy ne "" && $l < $pos_SNP4+10) || $heteroplasmy eq "") && $SNP eq "4" && ($pos_SNP ne 0 || ($pos_SNP4 > $pos_SNP+12) || ($extensions_before eq "yes" && $l > 12))) 
                 {

Original file line number	Diff line number	Diff line change
`@@ -10041,13 +10041,14 @@ sub align_hp`
`10041`	`10041`	`my @IUPAC = IUPAC($nucs{"A"},$nucs{"C"},$nucs{"T"},$nucs{"G"},$hp);`
`10042`	`10042`	`if ($IUPAC[0] eq "A" \|\| $IUPAC[0] eq "C" \|\| $IUPAC[0] eq "T" \|\| $IUPAC[0] eq "G")`
`10043`	`10043`	`{`
	`10044`	`+ $best_extension = $best_extension.$IUPAC[0];`
`10044`	`10045`	`}`
`10045`	`10046`	`else`
`10046`	`10047`	`{`
	`10048`	`+ $best_extension = $best_extension."N";`
`10047`	`10049`	`$SNP++;`
`10048`	`10050`	`}`
`10049`	`10051`	`$allele_percentage{$l} = $nucs{"A"}."+".$nucs{"C"}."+".$nucs{"T"}."+".$nucs{"G"};`
`10050`		`- $best_extension = $best_extension.$IUPAC[0];`
`10051`	`10052`	`}`
`10052`	`10053`	`elsif ((($heteroplasmy ne "" && $l < $pos_SNP4+10) \|\| $heteroplasmy eq "") && $SNP eq "4" && ($pos_SNP ne 0 \|\| ($pos_SNP4 > $pos_SNP+12) \|\| ($extensions_before eq "yes" && $l > 12)))`
`10053`	`10054`	`{`
`@@ -18432,13 +18433,14 @@ sub align_hp`
`18432`	`18433`	`my @IUPAC = IUPAC($A,$C,$T,$G);`
`18433`	`18434`	`if ($IUPAC[0] eq "A" \|\| $IUPAC[0] eq "C" \|\| $IUPAC[0] eq "T" \|\| $IUPAC[0] eq "G")`
`18434`	`18435`	`{`
	`18436`	`+ $best_extension = $best_extension.$IUPAC[0];`
`18435`	`18437`	`}`
`18436`	`18438`	`else`
`18437`	`18439`	`{`
`18438`	`18440`	`$SNP++;`
	`18441`	`+ $best_extension = $best_extension."N";`
`18439`	`18442`	`}`
`18440`		`- $allele_percentage_back{$l} = $A."+".$C."+".$T."+".$G;`
`18441`		`- $best_extension = $best_extension.$IUPAC[0];`
	`18443`	`+ $allele_percentage_back{$l} = $A."+".$C."+".$T."+".$G;`
`18442`	`18444`	`}`
`18443`	`18445`	`elsif ((($heteroplasmy ne "" && $l < $pos_SNP4+10) \|\| $heteroplasmy eq "") && $SNP eq "4" && ($pos_SNP ne 0 \|\| ($pos_SNP4 > $pos_SNP+12) \|\| ($extensions_before eq "yes" && $l > 12)))`
`18444`	`18446`	`{`