Suppose I have a paired-end data set from Illumina with 100 base pairs on each end. If any fragment is shorter than 200 base pairs, the ends of the two sequences will overlap when mapped to the genome. For example, if a particular fragment is 150 base pairs long, then the last 50 base pairs of read 1 will be the reverse complement of the last 50 base pairs of read 2.
So, which short-read mapping programs can handle such a case? And for ones that don't, how can I work around this problem?