Cropped reads larger than 75 bp

[ropolomx]

In the publication in Genome Research it says that the preprocessing includes "normalizing read lengths for SNAP alignment by cropping reads of length >75 to 75 bp". However, I am seeing SAM alignments that resulted from SNAP alignments where reads are 100 bp, even though I did not change the length in the configuration file. How can this be fixed? Thank you.