Commit 227fe686 authored by Daniel Barrell's avatar Daniel Barrell
Browse files

minor changes to regexes and layout

parent 7c94d80b
......@@ -327,17 +327,18 @@ SCAF: while(<TXT>){
# Create haplotype seq_region (calculate length from mapping data)
MAP: while(<MAPPER>){
next if(/^#/); #ignore comemnts
next if /^#/; # ignore comments
chomp;
my ($acc, $p_start, $p_end, $part, $type, $contig, $c_start, $c_end, $strand) = split;
#check if this is one of the new patches
# check if this is one of the new patches
if(!$name_to_seq_id{$acc}){
next MAP;
}
else{
print "About to process an agp line for ".$acc_to_name{$acc}."\n";
}
if($type =~ /[ADFGOPW]/){
if($type =~ /^[ADFGOPW]$/){
if($strand eq "+"){
$strand = 1;
}
......
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