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environment
Also fixes issue where the control marker keyword was wrong
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selected
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it's needed to store the proximal/distal markers for each position
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api/rqtl.py
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in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
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integrated into the script yet though)
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generate_rqtl_cmd and also made code check if output file already exists (so caching works)
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instead of just the output filename
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they don't have corresponding values
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generate_rqtl_cmd which returns the actual command and output path
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