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fDOG update to 0.1.35#49

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Merged

HannahBioI merged 62 commits intofdog_goes_assemblyBIONF/fDOG:fdog_goes_assemblyfrom masterBIONF/fDOG:masterCopy head branch name to clipboardJan 23, 2025

Commits

Commits on Mar 15, 2022

• fdogs accepts dots in seed filename

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Commits on Jun 13, 2022

• removed fdog assembly files

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Commits on Oct 12, 2022

• fixed addTaxon replacing pipe

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Commits on Jan 24, 2023

• 0.1.0 (#26)

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• updated README

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• fixed kimura distance devide by 0

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Commits on Jan 25, 2023

• added preparation runtime to fdogs.run

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Commits on Jan 26, 2023

• fix path to refspec fa; add amino to hmmbuild

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• save core jobs for fdogs.run to file

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• speed up preparation in fdogs.run

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• fix bug identify seed ID with reuseCore

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Commits on Jan 27, 2023

• reduce evalue for identify seed ID

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• version bump

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Commits on Feb 2, 2023

• sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff

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• sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff

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• v0.1.5 version bump

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• added fn desc

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• accept old folder names

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Commits on Feb 3, 2023

• add option to update json file to checkData

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• option to use different names for data folders

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Commits on Feb 6, 2023

• add several options to work with data paths

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• add several options to work with data paths; resolves: #28

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• add several options to work with data paths; resolves: #28

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Commits on Feb 14, 2023

• fix sorting hmm hits

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• fix check for pathconfig file

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Commits on Feb 17, 2023

• fix number of hmmhits core compilation

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Commits on Feb 20, 2023

• rename log fdogs.run

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Commits on Feb 22, 2023

• adapt evalue

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• adapt evalue

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Commits on Mar 10, 2023

• muscle5,checkBlast,ignoreAnnoCheck

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Commits on May 11, 2023

• check empty tmp dir before deleting in addTaxon

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Commits on May 25, 2023

• fixed output filename for muscle5

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Commits on Jun 12, 2023

• fixed mapping file for addTaxon

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Commits on Jun 15, 2023

• set seqlen limit for muscle5

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Commits on Jul 18, 2023

• added warning for no hmm hit

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Commits on Aug 15, 2023

• added check for invalid min-/maxDist; works with fasta36.3.8g

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• added check for invalid min-/maxDist; works with fasta36.3.8g

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• added check for invalid min-/maxDist; works with fasta36.3.8g

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• fixed worrking with old fasta36

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• added check for invalid min-/maxDist; works with fasta36.3.8g

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Commits on Aug 16, 2023

• added all searchTaxa to phyloprofile

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• changed orthID NA to fdogMA for manually added taxa

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• option to not added all taxa

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• Update CHANGELOG.md

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• check valid rank for refspec only

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Commits on Sep 19, 2023

• deactivate fas config output

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Commits on Dec 14, 2023

• fixed bug identical geneIDs btw search and refspec

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Commits on Dec 20, 2023

• fixed bug identical geneIDs btw search and refspec

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• option to validate hmm hits by sequence score

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• option to validate hmm hits by sequence score

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Commits on Dec 21, 2023

• option to validate hmm hits by sequence score

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Commits on Feb 12, 2024

• fixed search taxa list when using --coreTaxa

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Commits on Feb 28, 2024

• fixed bug identical geneIDs btw search and refspec

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Commits on Mar 12, 2024

• fixed mergeOutput for domains files

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Commits on Mar 14, 2024

• fixed mergeOutput

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Commits on Apr 22, 2024

• changed error msg for seed ident

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Commits on Jun 3, 2024

• added option to use user-defined annotool file

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Commits on Jun 6, 2024

• check duplicated ids in mergeOutput for fasta files

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Commits on Oct 28, 2024

• mergeOutput accepts .forward.domains

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Commits on Nov 12, 2024

• replace distDeviation by candidateScoreFactor

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Commits on Nov 21, 2024

• renamed candidateScoreFactor by candScoreFactor

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Commits on Dec 9, 2024

• moved demo data from uni to dropbox

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