/usr/share/hyphy/TemplateBatchFiles/MergeSites.bf is in hyphy-common 2.2.7+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | SetDialogPrompt ("Please choose the first data file:");
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
fprintf (stdout, "\n\nData Set 1:\n", ds);
if (IS_TREE_PRESENT_IN_DATA)
{
fprintf (stdout, "\nTree In Data:", DATAFILE_TREE);
}
SetDialogPrompt ("Please choose the second data file:");
DataSet ds2 = ReadDataFile (PROMPT_FOR_FILE);
while (ds2.species!=ds.species)
{
ChoiceList (userChoice,"Unequal number of sequences",1,SKIP_NONE,
"Choose Again", "Choose another datafile to merge",
"Merge Anyway", "Pad missing sequences with deletions");
if (userChoice<0)
{
return;
}
if (userChoice==1)
{
break;
}
DataSet ds2 = ReadDataFile (PROMPT_FOR_FILE);
}
fprintf (stdout, "\n\nData Set 2:\n", ds2);
DataSet dsCombined = Concatenate (purge,ds,ds2);
fprintf (stdout, "\n\nMerged Data Set:\n", dsCombined);
SetDialogPrompt ("Save resulting data set to:");
DataSetFilter dsf = CreateFilter (dsCombined,1);
fprintf (PROMPT_FOR_FILE,CLEAR_FILE,dsf);
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