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

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

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Commits on Feb 13, 2023

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

    …y by haplotypes. Added function to calculate reference length by haplotypes.
    @albidgy
    albidgy committed Feb 13, 2023
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  2. Added value ploid for --ambiguity-usage option

    Amy authored and Amy committed Feb 13, 2023
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  3. Merge remote-tracking branch 'origin/dipquast' into dipquast

    Amy authored and Amy committed Feb 13, 2023
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Commits on Feb 19, 2023

  1. Added ploid value to the help menu

    Amy authored and Amy committed Feb 19, 2023
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Commits on Feb 20, 2023

  1. Fixed calculation for reference length by haplotypes and added calcul… 

    …ation genome fraction by haplotypes.
    @albidgy
    albidgy committed Feb 20, 2023
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  2. Revert "Added ploid value to the help menu" 

    This reverts commit c9f3912.
    Amy authored and Amy committed Feb 20, 2023
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Commits on Feb 21, 2023

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

    Amy authored and Amy committed Feb 21, 2023
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Commits on Feb 27, 2023

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

    Amy authored and Amy committed Feb 27, 2023
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  2. Changed behavior for --ambiguity-usage ploid parameter

    Amy authored and Amy committed Feb 27, 2023
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Commits on Mar 9, 2023

  1. Fixed dictionaries filling for dipquast: dip_genome_by_chr, length_of… 

    …_haplotypes are filled in quast.py
    @albidgy
    albidgy committed Mar 9, 2023
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Commits on Mar 13, 2023

  1. Minor improvements

    Amy authored and Amy committed Mar 13, 2023
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  2. Added new penalty for translocation between haplotypes - INTERHAPLOTR… 

    …ANSLOCATION
    @albidgy
    albidgy committed Mar 13, 2023
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Commits on Mar 20, 2023

  1. Fixed penalty score for interhaplotypes translocation

    @albidgy
    albidgy committed Mar 20, 2023
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Commits on Mar 27, 2023

  1. Added a function that allows to find homologous chromosomes using the… 

    … mash tool
    @albidgy
    albidgy committed Mar 27, 2023
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  2. Fixed filling dictionary dip_genome_by_chr with haplotypes

    @albidgy
    albidgy committed Mar 27, 2023
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Commits on Apr 17, 2023

  1. Added reporting of interhaplotype translocations

    @ibragimovaamina
    ibragimovaamina committed Apr 17, 2023
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  2. Corrected mistake

    @ibragimovaamina
    ibragimovaamina committed Apr 17, 2023
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Commits on May 3, 2023

  1. Added choice of best alignment for ambiguity contigs and fixed naming

    @albidgy
    albidgy committed May 3, 2023
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Commits on May 4, 2023

  1. Improved speed of get_coords_for_non_overlapping_seq() function in di… 

    …putils.py
    @albidgy
    albidgy committed May 4, 2023
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Commits on May 6, 2023

  1. Fixed initialization of dict on defaultdict in diputils.py

    @albidgy
    albidgy committed May 6, 2023
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  2. Created main file dipquast.py for ploid genome analysis and added new… 

    … flag --ploid
    @albidgy
    albidgy committed May 6, 2023
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  3. Added dipquast.py

    @albidgy
    albidgy committed May 6, 2023
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Commits on May 9, 2023

  1. Added option --ploid_assembly_type to adapt the analysis to two types… 

    … of assemblies: phased and consensus; added test data for 2 types of ploid genome assembly
    @albidgy
    albidgy committed May 9, 2023
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  2. Fixed help info for --ploid-assembly-type option

    @albidgy
    albidgy committed May 9, 2023
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Commits on May 11, 2023

  1. Added a new diploid metric (# of missed heterozygosity)

    @ibragimovaamina
    ibragimovaamina committed May 11, 2023
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Commits on May 22, 2023

  1. Updated README.md with dipQUAST.

    @ibragimovaamina
    ibragimovaamina committed May 22, 2023
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Commits on Jun 3, 2023

  1. Partly updated manual.html with dipQUAST.

    @ibragimovaamina
    ibragimovaamina committed Jun 3, 2023
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Commits on Aug 21, 2023

  1. Added compiled Mash for linux. Fixed selection of the best ambiguity … 

    …contig considering IDY.
    @albidgy
    albidgy committed Aug 21, 2023
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  2. Added a method for determining haplotypes by conservative names of ch… 

    …romosomes that have haplotype_N in the name
    @albidgy
    albidgy committed Aug 21, 2023
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  3. Removed tmp variable

    @albidgy
    albidgy committed Aug 21, 2023
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