Fixed a bug that will duplicate some reads due to the region mechanism.

[CoREse]

Due to the region mechanism, some reads acrossing two regions would be parsed twice. This patch fixes that problem.

[Meltpinkg]

Hello, @CoREse Thanks for using cuteSV. The issue you mentioned above could lead to the same signatures extracted twice from the alignment. But in the clustering step of cuteSV, the same SV signatures which are from the same reads will be filtered and only remain one. So the duplicated reads won't influence the result of cuteSV.

Best, Shuqi