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