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Imported Upstream version 0.1.7~dfsg
[samtools.git]
/
misc
/
novo2sam.pl
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 "-") {
$q+=1;
}
if ($indeltype eq "-") {
- my $deletedbase = $2 if $string =~ /(\d+)\-([A-Z]+)/;
+ my $deletedbase = $2 if $string =~ /(\d+)\-([A-Z
a-z
]+)/;
if ($deleteflag == 0 ) {
$mdtag.="^";
}
if ($deleteflag == 0 ) {
$mdtag.="^";
}
@@
-172,12
+172,12
@@
sub indeltype {
my $string = shift;
my $insert="";
my $indeltype;
my $string = shift;
my $insert="";
my $indeltype;
- if ($string =~ /([A-Z]+)\>/) {
+ if ($string =~ /([A-Z
a-z
]+)\>/) {
$indeltype=">";
$insert=$1;
} elsif ($string =~ /\-/) {
$indeltype="-";
$indeltype=">";
$insert=$1;
} elsif ($string =~ /\-/) {
$indeltype="-";
- } elsif ($string =~ /\+([A-Z]+)/) {
+ } elsif ($string =~ /\+([A-Z
a-z
]+)/) {
$indeltype="+";
$insert=$1;
}
$indeltype="+";
$insert=$1;
}
@@
-204,10
+204,10
@@
sub cigar_method {
next if $string =~ />/;
my $pos = $1 if $string =~ /^(\d+)/;
next if $string =~ />/;
my $pos = $1 if $string =~ /^(\d+)/;
- if ($string =~ /\+([A-Z
]+)/) {
+ if ($string =~ /\+([A-Z
a-z]+)/) {
$indeltype="+";
$insert = $1;
$indeltype="+";
$insert = $1;
- }elsif ($string =~ /\-([A-Z]+)/) {
+ }elsif ($string =~ /\-([A-Z
a-z
]+)/) {
$indeltype="-";
$insert = $1;
}
$indeltype="-";
$insert = $1;
}