Commit e5e905a0 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

updates cn definitions

parent 56d7ffe2
...@@ -102,8 +102,12 @@ while (my $line = <IN>) { ...@@ -102,8 +102,12 @@ while (my $line = <IN>) {
print CNSO join("\t",$hash{chromosome},$hash{start},$hash{end}, print CNSO join("\t",$hash{chromosome},$hash{start},$hash{end},
$hash{log2},$hash{cn}),"\n"; $hash{log2},$hash{cn}),"\n";
next if ($hash{cn} == 2 && $hash{cn1} ne '' && $hash{cn2} ne '' && $hash{cn1} > 0 && $hash{cn2} > 0) || scalar(keys %genes) < 1; if (exists $hash{cn1} && exists $hash{cn2}) {
next if ($hash{cn} == 2 && $hash{cn1} eq '' && $hash{cn2} eq ''); next if (($hash{cn} == 2 && $hash{cn1} ne '' && $hash{cn2} ne '' && $hash{cn1} > 0 && $hash{cn2} > 0) || scalar(keys %genes) < 1);
next if ($hash{cn} == 2 && $hash{cn1} eq '' && $hash{cn2} eq '');
}else {
next if ($hash{cn} == 2 || scalar(keys %genes) < 1);
}
my $abtype = 'cnLOH'; my $abtype = 'cnLOH';
if ($hash{cn} < 2) { if ($hash{cn} < 2) {
if ($hash{cn} < 1 ) { if ($hash{cn} < 1 ) {
...@@ -116,8 +120,10 @@ while (my $line = <IN>) { ...@@ -116,8 +120,10 @@ while (my $line = <IN>) {
if ($hash{cn} > 6) { if ($hash{cn} > 6) {
$abtype = 'amplification'; $abtype = 'amplification';
} }
if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) { if (exists $hash{cn1} && exists $hash{cn2}) {
$abtype.= ' LOH'; if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
$abtype.= ' LOH';
}
} }
} else { } else {
$abtype = 'cnLOH'; $abtype = 'cnLOH';
......
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