Clipped reads not removed

[annecmg]

I was happy to find this tool which does exactly what I want: Remove reads with many clipped bases, but not in the beginning and end of contigs.
However, I find that too many reads remain in the mapping, I run the debug mode and here is one example of a read that should be BAD:

GOOD CHROM=GC00000017_11_p1:1..357 POS=149..299 CIGAR=89M62S L=0 R=0 | HL=0 SL=0 SR=62 HR=0 max=5)

The read has only 89M bases so I think POS should be 149..237 and the end of the contig (357) is not reached yet.