Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)

diff --git a/misc/novo2sam.pl b/misc/novo2sam.pl
index 3d3436c9534e315cd71ef9b8b5633289c63b0fd0..8b53c9efaf80cef817231111699b58a035049209 100755 (executable)
--- a/misc/novo2sam.pl
+++ b/misc/novo2sam.pl
@@ -149,7 +149,7 @@ sub mdtag {
                      $q+=1;
                }
                if ($indeltype eq "-") {
-                       my $deletedbase = $2 if $string =~ /(\d+)\-([A-Z]+)/;
+                       my $deletedbase = $2 if $string =~ /(\d+)\-([A-Za-z]+)/;
                        if ($deleteflag == 0 ) {
                                $mdtag.="^";
                        }
@@ -172,12 +172,12 @@ sub indeltype {
        my $string =  shift;
        my $insert="";
        my $indeltype;
-               if ($string =~ /([A-Z]+)\>/) {
+               if ($string =~ /([A-Za-z]+)\>/) {
                         $indeltype=">";
                         $insert=$1;
                 } elsif ($string =~ /\-/) {
                         $indeltype="-";
-                } elsif ($string =~ /\+([A-Z]+)/) {
+                } elsif ($string =~ /\+([A-Za-z]+)/) {
                         $indeltype="+";
                         $insert=$1;
                 }
@@ -204,10 +204,10 @@ sub cigar_method {
                next if $string =~  />/;
                my $pos = $1 if $string =~ /^(\d+)/;
                
-               if ($string =~ /\+([A-Z]+)/) {  
+               if ($string =~ /\+([A-Za-z]+)/) {       
                        $indeltype="+";
                        $insert = $1;
-               }elsif ($string =~ /\-([A-Z]+)/) {
+               }elsif ($string =~ /\-([A-Za-z]+)/) {
                        $indeltype="-";
                        $insert = $1;
                }