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Commits on Feb 22, 2024

• Release pangene-1.1 (r231)

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Commits on Feb 17, 2024

• r222: joint pseudogene by default

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• a new subcmd for analyzing outgroups

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Commits on Feb 16, 2024

• r220: output supporting assemblies

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• subsection on 100 human haplotypes

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Commits on Feb 9, 2024

• r215: use the new algorithm by default

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• calculate parent ID

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• search undirected neighbors

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• change the definition of bubbles

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• code refactoring, a little bit

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• backup

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• prepare for a new bb finding method

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Commits on Feb 6, 2024

• optionally use reference to add hidden tips

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Commits on Jan 29, 2024

• r193: test fake bubbles

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Commits on Jan 17, 2024

• parse Ensembl_canonical

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Commits on Jan 10, 2024

• filter mmseqs for checking overlaps

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Commits on Nov 8, 2023

• r188: generate PAF for dotplot

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Commits on Nov 6, 2023

• r187: discard readthrough genes by default

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Commits on Nov 3, 2023

• r186: allow to exclude by transcript names

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• r185: don't output bubbles with one allele

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• r184: parse GenCode annotations

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Commits on Oct 22, 2023

• r182: added calldiff

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• added call2html

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Commits on Oct 20, 2023

• added subcommands to pangene.js

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Commits on Oct 19, 2023

• exposed command-line option for parse-ensembl

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• parse Ensembl-formatted proteins

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Commits on Oct 13, 2023

• added -w

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Commits on Oct 3, 2023

• expose max_ext to CLI

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• fixed a misuse

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• don't output long gene list

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• code refactoring

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• report alleles

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Commits on Sep 22, 2023

• renamed UndirectedGFA to NetGraph

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• get genes in a bubble

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• another fix for things not in cycles

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