physlr-make: update rules to reflect new features

[jwcodee]

This PR contains updates that I missed when I updated the physlr-make file in the previous PRs #131 #140 . This PR also contains change to physlr-split-minimizers to work with ext.mol.tsv files.

[lcoombe]

Can you rebase this on master??

[jwcodee]

Yeah I forgot to update this branch before pushing.

EDIT: done

[aafshinfard]

@jowong4
At line 188, in help, the default value for mol_strategy is still distributed.

	@echo "	mol_strategy			molecule separation strategy [distributed]. Available options are bc, bc+k3, distributed, ext."

[aafshinfard]

there we have bug
when the user set mole_strategy to ext the makefile call the python code with --separation-strategy=ext which is not valid and previously I meant to use it to call the python code with distributed+sqcosbin in a single rule. so we can either remove ext from the help of physlr and make it a hidden keyword, or we can change the code so it translates ext to distributed+sqcosbin.

[jwcodee]

@afshinfard Are the new changes ok with you?

[aafshinfard]

@afshinfard Are the new changes ok with you?

Yes, prefect. Thanks.

[aafshinfard]

sorry, just found another refer to ext

@echo "	mol_strategy			molecule separation strategy [distributed+sqcosbin]. Available options are bc, bc+k3, distributed, ext."