Organize distmap launcher and add version argument

robmaz / distmap

Sequence alignment on Hadoop

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Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

Some organization for the Distmap launcher, including:

Re-order variables and GetOption map to pinpoint issues and remove unused variables
Document --reference-index-archive (but documented in Wikispaces)
Make $version a constant VERSION and add --version and -v to print version and exit.
Make help argument parsing more concise

robmaz commented 6 years ago

Has conflicts again, can you resolve and merge?

magicDGS commented 6 years ago

Rebased into latest master, @robmaz - ready to merge (if you want, make another pass to check everything to be sure)