Oshlack / STRetch

Method for detecting STR expansions from short-read sequencing data

MIT License

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Adding script to reformat STRs.tsv #51

Closed wdecoster closed 5 years ago

wdecoster commented 5 years ago

This pull request contains a script to reformat the STRs.tsv output:

Creates a pivot table listing the samples side by side
adding a variant identifier based on location and repeatunit
adding aggregate columns for e.g. maximal bpInsertion and minimal p_adj
sorting possible on chromosomal location or significance

It seems my code editor also removed some stray spaces and tabs from other files...

codecov-io commented 5 years ago

Codecov Report

Merging #51 into master will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #51   +/-   ##
=======================================
  Coverage   90.32%   90.32%           
=======================================
  Files           4        4           
  Lines         372      372           
=======================================
  Hits          336      336           
  Misses         36       36

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hdashnow commented 5 years ago

Would you mind doing a rebase -i against the latest master to merge all the minimap2 commits together? Since they cancel each other out they're just cluttering the history. You could just have a single commit changing the whitespace if you like, or not edit those files at all. Or if it's easier you could make a fresh branch off the master and either cherry-pick across the pivot script commits, or just do a new commit with just the script.

wdecoster commented 5 years ago

Yeah, I agree it's a bit of a mess. Will take care of it!