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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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continueCalling parsing problem #83

Open marqueda opened 4 years ago

marqueda commented 4 years ago

Dear Andy,

I tried to use the continueCalling function of Platypus (great idea to have such a function), but as I have been calling on several BAM files, which are comma-separated in the VCF header, Platypus cannot correctly parse the platypusOptions line, which it also does by comma separation. I assume this could be fixed with using another separator in the platypusOptions VCF header line?

Thank you for continuing to maintain Platypus!

Best wishes, David

marqueda commented 4 years ago

Dear Andy,

I found a (temporary) bugfix for this problem, by replacing lines 179 and 182 in the runner.py script... line 179: optionsStr = line.split("=")[1].replace("{", "").replace("}","") line 182: for option in optionsStr.split(","):

...with the following two lines: line 179: optionsStr = line.split("=")[1].replace("{", "").replace("}","").replace(",",";").replace("bam';","bam',") line 182: for option in optionsStr.split(";"):

This switches all option separators to semicolons and switches back the BAM file path separators to commas (which are needed as separators by the Platypus callVariants command). Not an elegant solution, but it works. The more elegant solution would be replace comma separators in the VCF header line for different Platypus options with semicolon separators.

Best wishes, David