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Explain every entry in the metadata file. #17
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This is in the paper, but needs to be reviewed for completeness. |
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I'm about to push the data to Zenodo and just went through all of the meta data in detail. I fixed a bunch of errors, but would you all mind looking through the data too to see if you notice any oddities? You can view the tables of data indexed by trial number here: |
I did not see any obvious errors, but have a couple of comments:
Ton On 11/26/2014 11:32 AM, Jason K. Moore wrote:
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The meta data is stored in a single file per trial (e.g., https://gist.github.com/moorepants/6bbc495128b181393023) and is located in that trial's directory. I did it this way, instead of using a proper database, to simplify things because no one in the lab seemed interested in using a real database to manage this. Thus, there is redundant "study" and "subject" data in each meta data file so that all the meta data for one trial is with the data files for that trial. The function I'd like to include all the trials we measured because they include potentially useful data. The code already exists that allows you to query trial numbers from the data I have. I could write some code to store the data in an HDF5 or sqlite database file and then the database can be queried with libraries that already exist instead of me writing custom bits for scraping a directory tree. |
It's OK to have the extra trials as long as it is not a puzzle for the Perhaps just this Table to generate for the paper: column 1: subject id number That presents a nice birds-eye view of the dataset and helps people find Ton On 11/26/2014 1:23 PM, Jason K. Moore wrote:
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Ok, I'll generate that table. |
This needs to be either in the GATK docs or in the paper or with the data.
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