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Update PhaME.pm#10

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rohith-molsys wants to merge 3 commits into
LANL-Bioinformatics:masterfrom
rohith-molsys:master
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Update PhaME.pm#10
rohith-molsys wants to merge 3 commits into
LANL-Bioinformatics:masterfrom
rohith-molsys:master

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@rohith-molsys

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Fix: large number of files fail to move in certain systems.

Minor Fix: coding flag was read as string hence further conditions always returned false.
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