#fix missed { in {c}
perl  -lne "BEGIN{$/=''}@ar=split /\s+/,$_;$k=join qq(\n),@ar[0..3];$h{$k}{s}.=' '. $ar[4];$h{$k}{c}+=$1 if $ar[4]=~/(\d+)/;END{print map{qq($_ $h{$_}{c} $h{$_}{s}\n\n)} keys %h}"    gen1.txt gen2.txt

@gi
AGAT
+
AAAA 2  1:1.txt 1:2.txt

@gi
CATT
+
AAAAA 3  3:1.txt

@gi
TACA
+
AAAA 2  2:2.txt

# infact the dumped datastructure is easily intellegible:
# in the oneliner h is for hash
# s is for string
# c for count (ah! never use single char variable names!)

perl -MData::Dump -lne "BEGIN{$/=''}@ar=split /\s+/,$_;$k=join qq(\n),@ar[0..3];$h{$k}{s}.=' '.$ar[4];$h{$k}{c}+=$1 if $ar[4]=~/(\d+)/;END{dd %h}"    gen1.txt gen2.txt

(
  "\@gi\nAGAT\n+\nAAAA",
  { c => 2, s => " 1:1.txt 1:2.txt" },
  "\@gi\nCATT\n+\nAAAAA",
  { c => 3, s => " 3:1.txt" },
  "\@gi\nTACA\n+\nAAAA",
  { c => 2, s => " 2:2.txt" },
)


#oh well we dont need @ar at all, perl -a at the rescue:

perl  -lane "BEGIN{$/=''}$k=join qq(\n),@F[0..3];$h{$k}{s}.=' '.$F[4];$h{$k}{c}+=$1 if $F[4]=~/(\d+):/;END{print map{qq($_ $h{$_}{c} $h{$_}{s}\n\n)} keys %h}"    gen1.txt gen2.txt


# ok i've nothing better to do this night..

perl  -lane "BEGIN{$/=''}map{$h{$_}{s}.=' '.$F[4];$h{$_}{c}+=$1 if $F[4]=~/(\d+):/}join qq(\n),@F[0..3]; END{print map{qq($_ $h{$_}{c} $h{$_}{s}\n\n)} keys %h}"    gen1.txt gen2.txt