SeqPrep and discarding reads

[Hena]

I've been testing SeqPrep (http://seqanswers.com/wiki/SeqPrep) for trimming adapters and merging reads. However I'm unsure why some reads get discarded. The command line is as follows:

SeqPrep -f s_5_1_sequence.txt.gz -r s_5_2_sequence.txt.gz -1 s_5_1-trimmed.fastq.gz -2 s_5_2-trimmed.fastq.gz -A AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -B AGATCGGAAGAGCGTCGTGTAGGGAAAGAGT -s merged.fastq.gz -L 1 -6 -E alignment.txt.gz

I'm assuming -L 1 would prevent removal of any reads (the help on command line differs abit from the wiki page). However reads still get removed. What causes this and what should I do to affect this?

[jp.]

any solution did you get ?

[Hena]

I found an answer to why it does discard reads even after minimum length.

https://github.com/jstjohn/SeqPrep/issues/3

Edit: If SeqPrep matches adapters but fails to do proper merge of reads, then it discards the reads. I suppose it would be possible to make a patch to prevent this functionality.