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

updates cn definitions

parent 56d7ffe2
......@@ -102,8 +102,12 @@ while (my $line = <IN>) {
print CNSO join("\t",$hash{chromosome},$hash{start},$hash{end},
$hash{log2},$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} 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 $abtype = 'cnLOH';
if ($hash{cn} < 2) {
if ($hash{cn} < 1 ) {
......@@ -116,9 +120,11 @@ while (my $line = <IN>) {
if ($hash{cn} > 6) {
$abtype = 'amplification';
}
if (exists $hash{cn1} && exists $hash{cn2}) {
if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
$abtype.= ' LOH';
}
}
} else {
$abtype = 'cnLOH';
}
......
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