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handle cases where the same tag sequence is seen in both index reads #865

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merged 1 commit into from
Jun 24, 2024
Merged

handle cases where the same tag sequence is seen in both index reads #865

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10 changes: 5 additions & 5 deletions bin/npg_qc_tag_sniff.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
q[?page%5Bnumber%5D=1&page%5Bsize%5D=500];

##no critic
our $VERSION = '0';
our $VERSION = '72.1.0';

sub usage {

Expand Down Expand Up @@ -200,12 +200,12 @@ sub showTags{
if ($revcomp) {
# revcomp match AND we are looking for revcomp matches AND we are looking for revcomp matches on this tag
if (@{$revcomps} && $revcomps->[$i]) {
$matches{$subtag}->{$id} = [$map_id,1,$original];
$matches{$subtag}->[$i]->{$id} = [$map_id,1,$original];
}
} else {
# not a revcomp match AND we are not looking for revcomp matches or we are not looking for revcomp matches on this tag
if (!@{$revcomps} || !$revcomps->[$i]) {
$matches{$subtag}->{$id} = [$map_id,0,$original];
$matches{$subtag}->[$i]->{$id} = [$map_id,0,$original];
}
}

Expand All @@ -222,8 +222,8 @@ sub showTags{
foreach my $i (0..$#subtags) {
my $subtag = $subtags[$i];
foreach my $id (sort {$a<=>$b} keys %{$groups[$i]}) {
if ( exists($matches{$subtag}->{$id}) ){
my ($map_id, $revcomp, $original) = @{$matches{$subtag}->{$id}};
if ( exists($matches{$subtag}->[$i]->{$id}) ){
my ($map_id, $revcomp, $original) = @{$matches{$subtag}->[$i]->{$id}};
print $revcomp ? REVERSE : q[];
printf "%2d(%3d %s) ", $id, $map_id, $original;
print $revcomp ? RESET : q[];
Expand Down
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