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fDOG update to 0.1.35 #49

Merged
merged 62 commits into from
Jan 23, 2025
Merged

fDOG update to 0.1.35 #49

merged 62 commits into from
Jan 23, 2025

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HannahBioI
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trvinh added 30 commits March 15, 2022 14:19
@trvinh
fdogs accepts dots in seed filename
a0747e0
@trvinh
removed fdog assembly files
20aa839
@trvinh
fixed addTaxon replacing pipe
d8eea1f
@trvinh
0.1.0 (#26)
055051f 
* create v0.1.0

* simplfying hamstr.pl

* first python conversion

* modified addTaxon and addTaxa

* added install/check dependencies

* rename data folders

* added runtime for core complilation
@trvinh
updated README
dd9a45c
@trvinh
fixed kimura distance devide by 0
8624f7d
@trvinh
added preparation runtime to fdogs.run
f984b26
@trvinh
fix path to refspec fa; add amino to hmmbuild
e728252
@trvinh
save core jobs for fdogs.run to file
2405698
@trvinh
speed up preparation in fdogs.run
9edaf9e
@trvinh
fix bug identify seed ID with reuseCore
8332690
@trvinh
reduce evalue for identify seed ID
8855db4
@trvinh
version bump
1edad42
@trvinh
sort hmm hits using domain scores; correct tree walking; setup force …
206def0 
…not delete data; correct profile output with fasOff
@trvinh
sort hmm hits using domain scores; correct tree walking; setup force …
ad2cbbd 
…not delete data; correct profile output with fasOff
@trvinh
v0.1.5 version bump
ad8741d
@trvinh
added fn desc
bfbc324
@trvinh
accept old folder names
4339bad
@trvinh
add option to update json file to checkData
198393d
@trvinh
option to use different names for data folders
ab5491b
@trvinh
add several options to work with data paths
7c3191a
@trvinh
add several options to work with data paths; resolves: #28
8bd2359
@trvinh
add several options to work with data paths; resolves: #28
bb185a3
@trvinh
fix sorting hmm hits
5785980
@trvinh
fix check for pathconfig file
f7c4cf8
@trvinh
fix number of hmmhits core compilation
03c9038
@trvinh
rename log fdogs.run
7798d15
@trvinh
adapt evalue
56995b1
@trvinh
adapt evalue
7e6bfbc
@trvinh
muscle5,checkBlast,ignoreAnnoCheck
052cf70
trvinh added 29 commits June 15, 2023 16:24
@trvinh
set seqlen limit for muscle5
a8541f8
@trvinh
added warning for no hmm hit
48372cf
@trvinh
added check for invalid min-/maxDist; works with fasta36.3.8g
a746c8f
@trvinh
added check for invalid min-/maxDist; works with fasta36.3.8g
c756ab0
@trvinh
added check for invalid min-/maxDist; works with fasta36.3.8g
553cdaa
@trvinh
fixed worrking with old fasta36
b7ec6fa
@trvinh
added check for invalid min-/maxDist; works with fasta36.3.8g
3e0859b
@trvinh
added all searchTaxa to phyloprofile
5cb0946
@trvinh
changed orthID NA to fdogMA for manually added taxa
e6ce3d1
@trvinh
option to not added all taxa
eb902a6
@trvinh
Update CHANGELOG.md
deeda8a
@trvinh
check valid rank for refspec only
5ccf824
@trvinh
deactivate fas config output
959e0a0
@trvinh
fixed bug identical geneIDs btw search and refspec
26bba47
@trvinh
fixed bug identical geneIDs btw search and refspec
9dc4fe9
@trvinh
option to validate hmm hits by sequence score
0404231
@trvinh
option to validate hmm hits by sequence score
e1f92f1
@trvinh
option to validate hmm hits by sequence score
82acd82
@trvinh
fixed search taxa list when using --coreTaxa
91edb37
@trvinh
fixed bug identical geneIDs btw search and refspec
1b4a778
@trvinh
fixed mergeOutput for domains files
359e739
@trvinh
fixed mergeOutput
a601990
@trvinh
changed error msg for seed ident
29afb52
@trvinh
added option to use user-defined annotool file
3893e66
@trvinh
check duplicated ids in mergeOutput for fasta files
e9340cf
@trvinh
mergeOutput accepts .forward.domains
26f2178
@trvinh
replace distDeviation by candidateScoreFactor
ed93866
@trvinh
renamed candidateScoreFactor by candScoreFactor
ea63637
@trvinh
moved demo data from uni to dropbox
1b7b930
@HannahBioI HannahBioI merged commit 430b7bb into fdog_goes_assembly Jan 23, 2025
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2 participants
@HannahBioI @trvinh