Merge pull request #2 from JulianJaffe/master

NOJIRA: Reconciliate repos
UCBG-328, UCBG-329: added filters to BedList and Collection Holdings
Merge branch 'master' of https://github.com/jblowe/Tools
PAHMA-843: barcode file processing; fix small glitch
UCBG-330: partial repairs to logic to retieve alives and deads. Probably we are not done yet...
Merge remote-tracking branch 'upstream/master'