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Commits on Jan 7, 2025

• string fix

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• generate tests updated for toytree

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• Merge branch 'master' of github.com:dereneaton/ipyrad

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• generate tests updated for toytree

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Commits on Jan 6, 2025

• "Updating ipyrad/__init__.py to version - 0.9.104

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• fix max_raw_reads_sample setter

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Commits on Dec 19, 2024

• analysis.bpp - update docs to remove refs to bpp.params

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Commits on Dec 17, 2024

• "Updating ipyrad/__init__.py to version - 0.9.103

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• Merge branch 'master' of https://github.com/dereneaton/ipyrad

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• Step 2 added _sample_max_raw_reads() and hackersonly.max_raw_reads_sample

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Commits on Dec 16, 2024

• cosmetic

  eaton-lab

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• bugfix wex again

  eaton-lab

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• Merge branch 'master' of github.com:dereneaton/ipyrad

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• bugfix for wex sample stats for one scaff or concat

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Commits on Dec 11, 2024

• Update 6-params.rst

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Commits on Nov 26, 2024

• debugging sample stats in wex

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Commits on Nov 25, 2024

• add func to view sample coverages after wex

  eaton-lab

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Commits on Nov 22, 2024

• digest genomes simplified a bit

  eaton-lab

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• window extracter write to fasta option added

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Commits on Nov 6, 2024

• change default impute method temporarily

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• fix the default pca impute_method

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• add analysis.utils.read_popsfile function to load imap from file

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Commits on Sep 23, 2024

• pca: fix impute_method logic so None means all 0s

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Commits on Sep 22, 2024

• snps_extracter allow to pass imap samples as pd.Index (makes groupby pop assignment easier)

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• pca impute_method for no imputation should be None and not False

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• pca: warn if numpy > 2.0

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• add muscle_version util

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Commits on Sep 6, 2024

• "Updating ipyrad/__init__.py to version - 0.9.102

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• fix SE loading to allow mixed .fq and .fastq file names

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Commits on Sep 3, 2024

• "Updating ipyrad/__init__.py to version - 0.9.101

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• Fix bug in SE sorted_fastqs

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Commits on Aug 28, 2024

• "Updating ipyrad/__init__.py to version - 0.9.100

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• Merge branch 'master' of https://github.com/dereneaton/ipyrad

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• Use the PE/SE information in the datatype param to determine whether to search for paired files.

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Commits on Aug 22, 2024

• hackers mask cut sites in s3

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