Added diputils.py. Added the ability to create a dictionary separatel…#236

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albidgy wants to merge 30 commits into

Commits on Feb 13, 2023

Added diputils.py. Added the ability to create a dictionary separately by haplotypes. Added function to calculate reference length by haplotypes.
albidgy
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Added value ploid for --ambiguity-usage option

Amy
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Amy
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Merge remote-tracking branch 'origin/dipquast' into dipquast

Amy
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Amy
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Commits on Feb 19, 2023

Added ploid value to the help menu

Amy
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Amy
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Commits on Feb 20, 2023

Fixed calculation for reference length by haplotypes and added calculation genome fraction by haplotypes.
albidgy
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Revert "Added ploid value to the help menu"

Amy
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Amy
committed

Commits on Feb 21, 2023

Added --ambiguity-usage "ploid" option to the help menu.

Amy
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Amy
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Commits on Feb 27, 2023

Added my very own little reference for testing --ambiguity-usage ploidy

Amy
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Amy
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Changed behavior for --ambiguity-usage ploid parameter

Amy
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Amy
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Commits on Mar 9, 2023

Fixed dictionaries filling for dipquast: dip_genome_by_chr, length_of_haplotypes are filled in quast.py
albidgy
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Commits on Mar 13, 2023

Minor improvements

Amy
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Amy
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Added new penalty for translocation between haplotypes - INTERHAPLOTRANSLOCATION
albidgy
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Commits on Mar 20, 2023

Fixed penalty score for interhaplotypes translocation
albidgy
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Commits on Mar 27, 2023

Commits on Apr 17, 2023

Commits on May 3, 2023

Added choice of best alignment for ambiguity contigs and fixed naming
albidgy
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Commits on May 4, 2023

Improved speed of get_coords_for_non_overlapping_seq() function in diputils.py
albidgy
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Commits on May 6, 2023

Commits on May 9, 2023

Commits on May 11, 2023

Added a new diploid metric (# of missed heterozygosity)
ibragimovaamina
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Commits on May 22, 2023

Updated README.md with dipQUAST.
ibragimovaamina
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Commits on Jun 3, 2023

Partly updated manual.html with dipQUAST.
ibragimovaamina
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Commits on Aug 21, 2023