makefile improvements

[lfalquet]

Dear Wai,

I see the following improvements to bring the Makefile to a more user-friendly tool.

a) add a PATH for the reads in the config file (as for the reference), and then create the simlinks automatically within the Makefile
b) calculate all the indexes for the reference automatically (bwa, samtools etc…) within the Makefile

These 2 automatic steps would already make life easier. ;-)
Laurent

[wyleung]

i'll look into this today