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Use Svart v2.0.0 and SilentGenes #39

Merged
merged 45 commits into from
Mar 22, 2022
Merged

Use Svart v2.0.0 and SilentGenes #39

merged 45 commits into from
Mar 22, 2022

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ielis
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@ielis ielis commented Mar 21, 2022 •
edited

Changes:

  • use Svart v2.0.0 and Silent genes to model genes, transcripts, and genomic regions
  • do not ask for the configuration file to simplify squirls-cli
  • add ID to tabular input/output

ielis and others added 26 commits September 20, 2021 20:11
@ielis
Use Svart v2.0.0
89065fc 
Signed-off-by: Daniel Danis <daniel.danis@jax.org>
@ielis
Merge branch 'development' into use_svart2
9e11b8e 
# Conflicts:
#	squirls-core/src/main/java/org/monarchinitiative/squirls/core/reference/StrandedSequence.java
@ielis
Use Svart v2.0.0-RC1
76f4b75
@ielis
Validate input alleles in annotate-csv. Add ID to tabular inputs/ou…
a2d3433 
…tputs
@ielis
Ingest *Gencode* and *RefSeq* genes into the data directory
aa6b696
@ielis
Replace TranscriptModel with Transcript
2962277
@ielis
Implement TranscriptModelServiceSg, setup autoconfiguration and boo…
844dcd6 
…tstrap to use the new implementation. Add LICENSEs for Jannovar and BigWig code
@ielis
Update banner
6f2a2c0
@ielis
Improve logging
8bf39c8
@ielis
Remove jannovar cache CLI parameter, implement `TranscriptModelServic…
a4bac3b 
…eSg`
@ielis
Move TranscriptModelService & Jannovar interval tree code to core
1e63124
@ielis
Hide the RandomForst constructor
7015550
@ielis
Remove deprecated TranscriptModel and the associated classes
8da7956
@ielis
Add files for generating JSON gene files
d599e19
@ielis
Let the user choose transcript category and feature source, create `S…
0ca6115 
…quirls`, work with `Gene`s instead of `Transcript`s
@ielis
Rename TranscriptCategories to TranscriptCategory, improve CLI lo…
c6bc36c 
…gging
@ielis
Report transcript filtering in HTML result
4dd0c1f
@ielis
Use silent genes v0.2.1
c8c57ca
@ielis
Ingest Jannovar transcript databases
5d92fa6
@ielis
Use Jannovar to provide transcripts of the TranscriptModelService
b955309
@ielis
Remove TranscriptCategory, ensure JannovarData is read only once
d690ff9
@ielis
Remove versioned assembly, do not use config file for running analysis
5159df5
@ielis
Fix failing tests in the autoconfigure module
b0a67f1
@ielis
Remove the generate-config command
7836776
@ielis
Update CLI descriptions
9bd192b
@ielis
Use silent genes v0.2.3
2eddfd5
@ielis ielis added the enhancement New feature or request label Mar 21, 2022
@ielis ielis self-assigned this Mar 21, 2022
@ielis ielis merged commit 984b58c into development Mar 22, 2022
@ielis ielis deleted the use_svart2_and_silent_genes branch March 22, 2022 11:45
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