Fix non-mandatory prefix option

[nylander]

Dear @BenoitMorel !

Currently, the -p (prefix) parameter is non mandatory and not set with a default value. When running your minimal example ./asteroid -i GENE_TREES, this will result in "hidden" output files (.allTrees.newick, .bestTree.newick, .scores.txt).

One can solve this in several ways: Check for prefix as a mandatory parameter and stop if not provided, or set a fixed default prefix string if prefix is not provided, or base the prefix on the input. Adding the lines below to Arguments.cpp will do the latter.

Cheers Johan

---

Change (starting at line 56):

  if (inputBSGeneTreeFile.size() == 0) {
    inputBSGeneTreeFile = inputGeneTreeFile;
  }   

to

  if (inputBSGeneTreeFile.size() == 0) {
    inputBSGeneTreeFile = inputGeneTreeFile;
  }
  if (prefix.empty()) {
    prefix = inputGeneTreeFile;
  }

[BenoitMorel]

Hi Johan, Thank you very much for spotting this! I just applied the fix that you suggested. Best, Benoit

Le jeu. 15 févr. 2024 à 15:36, Johan Nylander @.***> a écrit :

Dear @BenoitMorel https://github.com/BenoitMorel !

Currently, the -p (prefix) parameter is non mandatory and not set with a default value. When running your minimal example ./asteroid -i GENE_TREES https://github.com/BenoitMorel/Asteroid#running-asteroid, this will result in "hidden" output files (.allTrees.newick, .bestTree.newick, .scores.txt).

One can solve this in several ways: Check for prefix as a mandatory parameter and stop if not provided, or set a fixed default prefix string if prefix is not provided, or base the prefix on the input. Adding the lines below to Arguments.cpp https://github.com/BenoitMorel/Asteroid/blob/main/src/asteroid/Arguments.cpp will do the latter.

Cheers Johan

Change (starting at line 56):

if (inputBSGeneTreeFile.size() == 0) { inputBSGeneTreeFile = inputGeneTreeFile; }

to

if (inputBSGeneTreeFile.size() == 0) { inputBSGeneTreeFile = inputGeneTreeFile; } if (prefix.empty()) { prefix = inputGeneTreeFile; }

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