Commit 92fbc971 authored by no_author's avatar no_author
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parent 6d815d0c
......@@ -541,75 +541,6 @@ sub match_sequences {
$seq_qualities_r2 = substr $seq_qualities_r2, $start2, $cut_len2;
}
}
# trim the barcode
# if ($trim) {
# if ($barcodes_at_bol){
# $start=$barcodes_length+$adapt;
# $stop=$seq_len;
# } elsif ($barcodes_at_eol) {
# $start=0;
# $stop=$seq_len-$adapt;
# }
#
# #~ warn $seq_len," ",$barcodes_length;
## if ($adapt && $barcodes_at_bol){
## $start=$barcodes_length;
## $stop=$seq_len;
## }elsif ($adapt && $barcodes_at_eol){
## $start=0;
## $stop=$seq_len;
## }elsif ($barcodes_at_bol){
## $start=$barcodes_length+1;
## $stop=$seq_len;
## }elsif ($barcodes_at_eol){
## $start=0;
## $stop=$seq_len-1;
## }
# warn "position of fragment to keep : $start, $stop \n" if $debug;
# if ($paired==1 && $barcodes_at_eol){
# $seq_bases_r2 = substr $seq_bases_r2, $start, $stop;
# } else {
# $seq_bases = substr $seq_bases, $start, $stop;
# }
#
# if ($fastq_format) {
# if ($paired==1 && $barcodes_at_eol){
# $seq_qualities_r2 = substr $seq_qualities_r2, $start, $stop;
# } else {
# $seq_qualities = substr $seq_qualities, $start, $stop;
# }
# }
# }
#
# # trim both read
# if ($trim2){
# my $start;
# my $stop;
# my $stop2;
# if ($adapt && $barcodes_at_bol){
# $start=$barcodes_length;
# $stop=$seq_len;
# $stop2=$seq_len_r2;
# }elsif ($adapt && $barcodes_at_eol){
# $start=0;
# $stop=$seq_len;
# $stop2=$seq_len_r2;
# }elsif ($barcodes_at_bol){
# $start=$barcodes_length+1;
# $stop=$seq_len;
# $stop2=$seq_len_r2;
# }elsif ($barcodes_at_eol){
# $start=0;
# $stop=$seq_len-1;
# $stop2=$seq_len_r2-1;
# }
# $seq_bases = substr $seq_bases, $start, $stop;
# $seq_bases_r2 = substr $seq_bases_r2, $start, $stop2;
# if ($fastq_format){
# $seq_qualities = substr $seq_qualities, $start, $stop;
# $seq_qualities_r2 = substr $seq_qualities_r2, $start, $stop2;
# }
# }
}
if ( (!defined $best_barcode_ident) || ($best_barcode_mismatches_count>$allowed_mismatches)){
......
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