Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

split "variant_details" into respective columns #7

Open
kwkroll32 opened this issue Feb 8, 2016 · 1 comment
Open

split "variant_details" into respective columns #7

kwkroll32 opened this issue Feb 8, 2016 · 1 comment
Assignees

Comments

@kwkroll32
Copy link
Collaborator

Invent a new output type like variant_details. Rather than making a comma-separated string of VF and DP for common mutations, add a new column for each duplicate. Only permits 1 sample per row.

Modify config to support new format and distinguish between variant calls. "source" will be re-named "format" to clearly identify the parsing module that should be used. The new value of "source" will be identical to "format," unless a sample has multiple VCFs from the same "format." In this case, "source" will have distinguishing values appended to it, i.e. [samtools.a, samtools.b, samtools.c] while "format" would be [samtools, samtools, samtools]. These "source" values will be used to name the specific columns in the new output mode.

@kwkroll32 kwkroll32 self-assigned this Feb 8, 2016
@jblachly
Copy link
Member

jblachly commented Feb 8, 2016

As this introduces a potentially-breaking change into the JSON config file (renaming source-> format) we should version the config file

kwkroll32 pushed a commit that referenced this issue Feb 8, 2016
…f the code accordingly. source is renamed to format, and the new value of source is used to determine column names in output. the output value source has been renamed to fn for clarity.
kwkroll32 pushed a commit that referenced this issue Feb 10, 2016
kwkroll32 pushed a commit that referenced this issue Feb 10, 2016
…dataframe. caused crashes in other output modules.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants