Overlapper SE file has no IDs and quality strings appear to be wrong and/or made up of sequences about htstream

[samhunter]

It is difficult to see in the text I pasted above, but view it fixed-width in a txt editor. It seems like the last piece of the quality string is the read!

[dstreett]

Copy paste error

finalQual += seq2.substr(maxLoop, r2.getLength() - maxLoop);

Should have been . . .

finalQual += qual2.substr(maxLoop, r2.getLength() - maxLoop);

[samhunter]

ID text still blank:

@id
ATGCTCACTACCACTCTCTCCGTACTGGAATATTCATCTACTCCCATTTTGCTGACTCTTATACCTCTCAGCGACATTTCCGTGCTTGGGGTCATATCAGGCAATATTCCGATCATTCCCATTACACTGTCAATGGGTTCAATCCCCCAGTTCTGGAAAAGCACTTTTGCATCCTTTTGGAAATGCCTCAAGAGTTGGTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id
TTTCCCCAACGATTGCTCCCTCCTCAGTGAAAGCCCTTAGTAGTATCAAAGTTTCTAATCGATTAAAGATCACACTGAAGTTCGCTTTCAGTATAATGTTCTTTTCCATGATCGCCTGGTCCATTCGCACATAAAGAGGGCCTATTATCTTTTGCCTAGGCATGAGCATGAACCAGTCTCGTGACATTTCCTCGAGGGTCATGTCAGCTATGT
+
"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

[dstreett]

It is a feature to reduce memory. ;) Just kidding, Fixed in N-Remover, will close once merged into master.