Prevent extension beyond F and R read starts

[dshivak]

Hi:

Is there an option to prevent extension of the merged sequence beyond the F and R start termini? We're ending up with a lot of partial adapter cruft (4-6bp) at one end if the F read is longer but isn't long enough to match the whole adapter. If not, would it be possible to add this as a feature?

Example test where longer F read appends cruft beyond R start:
SeqPrep -f test.fq -r testR.fq -1 test1 -2 test2 -s testmerge.fq
Processing reads... |
Pairs Processed: 1
Pairs Merged: 1
Pairs With Adapters: 0
Pairs Discarded: 0
CPU Time Used (Minutes): 0.000000

Forward:
@FOO
GAAAAGCTCCTGAGGTGTAGACGCCAACTCTCTCTAGCTCGCTAGTGGGTTGCAGGAGGTGCTTACGCATGTTTGTTTCTTTGCTGCCGTCTTCCAGTTGCCCCCCCCCCCCCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Reverse:
@FOO
CAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Merged:
@FOO
GAAAAGCTCCTGAGGTGTAGACGCCAACTCTCTCTAGCTCGCTAGTGGGTTGCAGGAGGTGCTTACGCATGTTTGTTTCTTTGCTGCCGTCTTCCAGTTGCCCCCCCCCCCCCC
+
]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]IIIIIIIIIIIIII

Thanks for the great program.

Dave S.