adds option to extract barcode from read2 only #630
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IanSudbery
reviewed
Mar 12, 2024
| @@ -542,7 +532,7 @@ def __call__(self, read1, read2=None): | |||
| # Check for regex is more complex. | |||
| # Reads too short with regex pattern will silently fail to match | |||
| if self.method == "string": | |||
| if(len(read1.seq) < len(self.pattern)): | |||
| if(self.pattern and (len(read1.seq) < len(self.pattern))): | |||
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@TomSmithCGAT Should there not be an equivalent of this for self.pattern2 and len(read2.seq)?
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Yes. Good point. I'll add that
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Ah, it's already there! See line 540
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Yep. Tests all run OK and new tests include mode=string and mode=regex. By 'And documented?', do you mean is the new option to just use read2 only documented? If so, yes, usual documentation in the tool, plus FAQs. |
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Sorry, I mean that if it were only available in regex mode is that documented. No worries if it works in both. |
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This adds the option
--read2-onlyforextractandwhitelistto only extract barcodes from read2.See #522 for motivation