Commit 6d815d0c authored by no_author's avatar no_author
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parent bd9e9d79
...@@ -456,7 +456,7 @@ sub match_sequences { ...@@ -456,7 +456,7 @@ sub match_sequences {
my $cut_len = $seq_len; my $cut_len = $seq_len;
my $start2 = 0; my $start2 = 0;
my $cut_len2 = $seq_len_r2; my $cut_len2 = $seq_len_r2;
warn $start , " " , $cut_len , " " , $start2 , " " , $cut_len2; # warn $start , " " , $cut_len , " " , $start2 , " " , $cut_len2;
#Try all barcodes, find the one with the lowest mismatch count #Try all barcodes, find the one with the lowest mismatch count
if ($barcodes_at_bol) { if ($barcodes_at_bol) {
$sequence_fragment = substr $seq_bases, 0, $barcodes_length; $sequence_fragment = substr $seq_bases, 0, $barcodes_length;
...@@ -500,7 +500,7 @@ sub match_sequences { ...@@ -500,7 +500,7 @@ sub match_sequences {
#~ $sequence_fragment = reverse_complement $sequence_fragment; #~ $sequence_fragment = reverse_complement $sequence_fragment;
#~ warn "sequence fragment revcomp: $sequence_fragment \n" if $debug; #~ warn "sequence fragment revcomp: $sequence_fragment \n" if $debug;
} }
warn $start," ", $cut_len, " ",$start2, " ",$cut_len2; # warn $start," ", $cut_len, " ",$start2, " ",$cut_len2;
foreach my $barcoderef (@barcodes) { foreach my $barcoderef (@barcodes) {
my ($ident, $barcode) = @{$barcoderef}; my ($ident, $barcode) = @{$barcoderef};
...@@ -806,7 +806,7 @@ sub open_and_detect_input_format ...@@ -806,7 +806,7 @@ sub open_and_detect_input_format
} else { } else {
die "Error: unknown file format. First character = '$first_char' (expecting > or \@)\n"; die "Error: unknown file format. First character = '$first_char' (expecting > or \@)\n";
} }
warn "len1: ", $seq_len, "; len2: ", $seq_len_r2, " ;barcode len: ", $barcodes_length, "; no adapt: ", $adapt; # warn "len1: ", $seq_len, "; len2: ", $seq_len_r2, " ;barcode len: ", $barcodes_length, "; no adapt: ", $adapt;
} }
sub doc() sub doc()
......
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