The ends justify the means

This fixes behaviour and contig ends again, and simplifies the code/logic so I don't confuse myself with double negatives again.

Out by one

Fix an important bug where soft-clipped reads were discarded if at start of contig, due to confusion over 0-based and 1-based coordinates. Reads at end of contigs were correctly handled.

Sorry.

First release

A standalone Perl script which acts as a SAM -> SAM pipe to filter soft/hard clipped reads.