Quotes all paths in mkdir calls #3
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This addresses the issue in which the shell expands unquoted paths passed to mkdir and thereby fails to create paths when they contain wildcard characters that happen to match another existing path. One failure that this fixes is that output directories are not always created when chromosome names contain '*' characters, such as when running against the HLA* sequences. An example of the failure would be if an output directory: /out/all/HLA-A*31:01:02 has been created first, and subsequently another directory /out/all/HLA-A*01:02 is attempted to be created, prior to this fix it would not be created because `mkdir -p /out/all/HLA-A*01:02` is expanded by the shell to match the existing directory (i.e. it is equivalent to `mkdir -p /out/all/HLA-A*31:01:02`, and the desired output directory is not created. I went ahead and quoted *all* instances of paths passed to mkdir because I'm pretty sure there is never a time when you want wildcard expansion when creating directories.
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This addresses the issue in which the shell expands unquoted
paths passed to mkdir and thereby fails to create paths when
they contain wildcard characters that happen to match another
existing path. One failure that this fixes is that output
directories are not always created when chromosome names contain
'' characters, such as when running against the HLA sequences.
An example of the failure would be if an output directory:
/out/all/HLA-A_31:01:02 has been created first, and subsequently
another directory /out/all/HLA-A_01:02 is attempted to be created,
prior to this fix it would not be created because
mkdir -p /out/all/HLA-A*01:02is expanded by the shell tomatch the existing directory (i.e. it is equivalent to
mkdir -p /out/all/HLA-A*31:01:02, and the desired outputdirectory is not created.
I went ahead and quoted all instances of paths passed to mkdir
because I'm pretty sure there is never a time when you want
wildcard expansion when creating directories.