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

[samhunter]

@id
ATGCTCACTACCACTCTCTCCGTACTGGAATATTCATCTACTCCCATTTTGCTGACTCTTATACCTCTCAGCGACATTTCCGTGCTTGGGGTCATATCAGGCAATATTCCGATCATTCCCATTACACTGTCAATGGGTTCAATCCCCCAGTTCTGGAAAAGCACTTTTGCATCCTTTTGGAAATGCCTCAAGAGTTGGTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id
TTTCCCCAACGATTGCTCCCTCCTCAGTGAAAGCCCTTAGTAGTATCAAAGTTTCTAATCGATTAAAGATCACACTGAAGTTCGCTTTCAGTATAATGTTCTTTTCCATGATCGCCTGGTCCATTCGCACATAAAGAGGGCCTATTATCTTTTGCCTAGGCATGAGCATGAACCAGTCTCGTGACATTTCCTCGAGGGTCATGTCAGCTATGT
+
"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id
NCGCCAAATATGCCTCTAGTTTGTTTCTCTGGCACATTCCGCATTCCTGTTGCCAATTTCAGAGTGTTTTGCTTAACATATCTGGGACAGACCCCATATGTGATCCTGTTTACATTTTGAAAGGGTTTGTCATTGGGAATGCTTCCATTTGGAGTAATGCATTCAGATTTGCAATTGACAATGGGTGCATCTGATCTCATTATTGAGCTTTTCCCACTCTGTATTTTGAAGTAACCCCGAGGGGCAATTAGATTCCCTGTGCTGTTAATCAAAAGTATGTCTCCCGGTTTTACTATTGT
+
#<0<BHIHHHHEGHHEHHHI?GGHIIEEHIE1DHHIIFHHFCDHEHEH7III4IIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII=;GI<<IIGIIIIIIATTCCCTGTGCTGTTAATCAAAAGTATGTCTCCCGGTTTTACTATTGT
@id
GGGCACCCCAGCTCAATCCTATTGATGGACCACTACCTGAAGATAATGAACCAAGTGGGTATGCACAAACAGACTGTGTCCTGGAGGCCATGGCTTTCCTTGAAGAATCCCACCCAGGGATATTTGAGAATTCATGCCTTGAAACAATGGAAATTGTCCAACAAGCAAGGGTGGATAAACTAACTCAGGGTCGCCAGACTTATGATTGGACATTAAATAGAAATCAACCGGCAGCAACTGCATTGGCCAACACCATAGAAGTTTTTAGATCAAATGGTCTCACAGCTAATGAGTCAGGAAGGCTAATAGATTTCTTAAAAGATGTAATGGAATCAATGGATAAAGAGGAAATAGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGGGATAACATGACCAAGAAGATGGTCACACAA
+
DCDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIHIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIACCATAGAAGTTTTTAGATCAAATGGTCTCACAGCTAATGAGTCAGGAAGGCTAATAGATTTCTTAAAAGATGTAATGGAATCAATGGATAAAGAGGAAATAGAGATAACAACACACTTTCAAAGAAAAAGGAGAGTAAGGGATAACATGACCAAGAAGATGGTCACACAA
@id
AATGTACTCAAATGCAAATGTTGCACCTAATGTTGCCTTTTTGGCAGGCCCACATAATGAACCCCAGCAGAACAACACAAAGCAAAAAGCATGACATGGCAAAGGAAATCCATAGGATCCAATCTTTGTATCCTGACTTCAGCTGAACACCTTTGATCTGGAACCGATTGCTTAATGCCTCGTCTCTGTATAC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id
CCTCTGCTGCTTGTTCACTTGACCCAGCCATTTGTTCCATGGCCTTAGCTGTTGTGCTGGCTATTACCATTCTGTTCTCGTGCCTGATTAGTGGATTGGTTGTTGTCACCATTTGTCTATGAGATCGATGCTGGGAATCAGCAATCTGTTCACAGGTTGCGCATACCAGACCAAATGCCACCTCAGTGGCGACAGTCCCCATTCTGTTGTATAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id
NCAGAATGCCCTCAATGGGAATGGTGACCCAAACAACATGGACAAGGCAGTCAAACTGTATAGGAAACTAAAACGAGAAATAACATTCCATGGGGCCAAAGAAGTAGCACTCAGTTATTCTGCCGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGAATGGGGACTGTCGCCACTGAGGTGGCATTTGGTCTGGTATGCGCAACCTGTGAACAGATTGCTGATTCCCAGCATCGATCTCATAGACAAATGGTGACAACAACCAATCCACTAATCAGGCACGAGAACAGAATGGTAATAGCCAGCACAACAG
+
#<DDDIGHHHHIIIIIHHIIHIHHIEHIHIHHIIIIHHHIHIIIIHIIIHCEHIHHHIHHIHIIHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"AAATGGTGACAACAACCAATCCACTAATCAGGCACGAGAACAGAATGGTAATAGCCAGCACAACAG
@id

[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.