Merge branch 'master' of https://github.com/mdozmorov/RepeatSoaker
Merge branch 'master' of https://github.com/mdozmorov/RepeatSoaker
Merge branch 'python'
Merge branch 'master' of https://github.com/mdozmorov/RepeatSoaker
Merge remote-tracking branch 'gh_upstream/master' into upstream
Adds setuptools
Add bedtools based version...
Changes position matches overlap check to use dict

An attempt to not create & recreate sets in an attempt to speed up the
"hot" code of comparing the overlap positions
Fixes slow dict to dict & then len

Now just "count" the items there quickly that are true
Moves percentage calculation outside heavy loop

Not much, but with zillions of rows of BIG DATA ever little calculation
adds up on the CPU
Merge pull request #1 from oklasoft/change_position_overlap_check

Possible slightly faster overlap match position check
Correcting bedtools intersect command. Adjusting Readme to reflect bedtools implementation of RepeatSoaker
Fixes #2 by removing the *.gz files

If one really wanted it could be purged back from old history of the
repository back in time with all manner of git crazy voodoo
Merge pull request #3 from oklasoft/fix_remove_gz_files

Fixes #2 by removing the *.gz files (hopefully, forever)
Adds a bit of defense for non zero exits

Just for fun I'll add in a bit for quicker failing, no sense in
continuing on if something isn't happy
Add quick check for bedtools & samtools in PATH

Again just a bit bored and figured why not be safe
Adds pipefailing too

Really since the samtools is piped we need to fail with there as well
Merge pull request #4 from oklasoft/add_bedtools_quick_fail

Making the script more foolproof
Fixes incorrect & silent exit 1

Was missing an extra set of () to keep that silly exit 1 from sneaking
out & getting running too often
Merge pull request #5 from oklasoft/fix_bedtools_over_zealous_exit

Fix bedtools over zealous exit