PcrClipReads: reads with already soft clipped bases

[alborm]

Hello Pierre,

Subject of the issue

I am using PcrClipReads to clip primers. I see some problems when the read starts or ends with soft clipped bases in readClipper().

Region__||---------------------------------------||____ Read:____<SSSSS......................................................_____ strand -

It seems that because soft clipped bases do not consumeReferenceBases, more bases are clipped than expected.

Expected behaviour

Only soft clip the bases outside of the region

Actual behaviour

Clips more bases from the end of the read.

Thanks.