Add VCF Comparison Program #8
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* initial commit, scratch work using pandas * redoing the file reading/parsing logic. Also added vcf data files to catalog * created file info object, started work on comparisons * Made changes to fileInfo object and began logic to grab genotype * Changed file objects, improved position alignment * Comparisons seem to be working, cleaned up code * improved methodology for setting file info in VCF * made script for looking at overlapping positions * more program cleaning, added pos comps for vcfs * began implementation of multi running VCFs * logic for readers to be used in a with statement. added .gz streaming * Created base class for readers * Added more error handling and alignment checks * moved functions to new util file, improved gt methods * added logic for custom errors, simplified reader read method * Created new class that uses VCFReader as super, removed internal self.fields use * cleaned up mainloop, fixed chrom order check * fixed error with straglr output, more method cleaning/debugging * restructured folders for cleanliness
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Initial version of the VCF comparison program. Still a a lot of known issues, but it is in a relatively workable state. Main problems still in this version include issues with handling of position-only files and issues with the 1 and 0 based offsets causing no 0 distances for the levenshtein comparisons