Fix TE-locate reference detection output

TE-locate outputs a length of insertion for reference TEs.
Unfortunately this can occasionally go over the end of the chromosome
so cannot be used in the results with genome browsing.
Script to pass through only correct SAM mappings

bwa sometimes (rarely) creates mappings where the sequence length and
CIGAR values are inconsistent. This scripts discards these reads to
prevent errors further in the pipeline.
Remove edited TEMP scripts
Use the SAM correcting script on bwa output
Change to new version of RelocaTE
Deal with uncertain predictions

Also changes naming conventions of TE insert predictions