Switch TEMP output to using junction annotations
Prevent chance of file overlap in parallel runs

There was a very slim chance of temporary files causing problems in
parallel runs during the parsing of results phase of mcclintock. These
have been moved in to sample specific folders to avoid this.
Updated analysis to run on 6 methods where needed
No point producing logos which are deleted after
Filter for TE insertions near to reference TEs
Add filtering step to PoPoolationTE
Added median insert size calc

Also reduced allowed mismatches in TEMP alignment to TE database.