Hotspot v4.1.0

This is release 4.1.0 of hotspot. The most substantive changes for this distribution include better
behavior on errors. Previously some scripts would continue to run if an error or abnormal exit occurred within its bounds. For details, see the CHANGES document at the top level of the distribution.

Hotspot v4.0.0

This is release 4.0.0 of hotspot, and should match nearly exactly the v4 release that was previously available on the hotspot page,

http://www.uwencode.org/proj/hotspot/

The only differences from that release should be in the example script and configuration file in the pipeline-scripts/test directory. All path names have been replaced with something more obviously fake. Also, the runhotspot file now downloads the test bam file if necessary, rather than assuming it is in the data directory, where it is no longer stored. This is to avoid using the Github repository to store large data files.