Mercurial > repos > tiagoantao > barcode_stacks
diff barcode_sort.pl @ 6:5cd3cc89bf59 draft
planemo upload commit 80e74122bff9cbc1d172f920b164d6db9c028e7b
| author | tiagoantao |
|---|---|
| date | Tue, 29 Mar 2016 12:45:39 -0400 |
| parents | d838c6a2ec0f |
| children | 2c843c8df821 |
line wrap: on
line diff
--- a/barcode_sort.pl Tue Mar 29 12:08:53 2016 -0400 +++ b/barcode_sort.pl Tue Mar 29 12:45:39 2016 -0400 @@ -8,6 +8,10 @@ # note this is the length of what's left after enzyme digestion, NOT the full length of the enzyme recognition site # the program expects all correct forward reads to follow the pattern: $n initial nucleotides, then $b nucleotides of barcode, then $e nucleotides of the cutsite +my $is_resilient; + +$is_resilient = $ARGV[5]; # true if is resilient to errors + open (IN, $ARGV[0]); # read file with barcodes my %counts = (); # make a hash of barcodes that will be searched while(<IN>) { # counts of each barcode can be tracked with this hash, with a few more lines of code below