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UCSF-DSCOLAB / data_processing_pipelines

A repository to store the existing pipelines to process the various CoLabs datasets
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BugFix for inconsistent column order in gtcheck.out #87

Closed dtm2451 closed 2 months ago

dtm2451 commented 2 months ago

In the genotype matching step, I noticed my dataset had reversed column ordering compared to what the pipeline expected. The pipeline expects freemuxlet clusters will exist in the 2nd column and sample ids will exist in the 3rd column of gtcheck.out files, but for me the sample ids were in column 2 and the freemuxlet clusters were in column 3. Thinking there's inherent inconsistency, this PR adds an attempt to use the opposite ordering if the initial expectation yields 0 rows.

Note: Only touches the "1.18" version of the code

erflynn commented 2 months ago

Thanks for fixing this! Good to go ahead and merge :)