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TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis #2190

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TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis #2190

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5d10e1b
analysis: update mutational signature to biodata changes, #TASK-2242,…
jtarraga Nov 3, 2022
5a58318
analysis: generate CLI automatically, #TASK-2242, #TASK-2243
jtarraga Nov 3, 2022
484776d
analysis: major improvements in sample quality control (mutational si…
jtarraga Nov 4, 2022
eef1601
analysis: updae mutational signature query and generate CLI, #TASK-22…
jtarraga Nov 4, 2022
7988a47
analysis: add log message, #TASK-2242, #TASK-2243
jtarraga Nov 4, 2022
80bab76
analysis: raise an exception when running a mutational-signature-quer…
jtarraga Nov 4, 2022
cf969cb
analysis: save mutational signature and fitting (as data model files)…
jtarraga Nov 8, 2022
abd3897
Merge branch 'release-2.4.x' into TASK-2242
jtarraga Nov 8, 2022
cd4c96c
analysis: remove HS metrics from alignment QC analysis, and generate …
jtarraga Nov 9, 2022
fedc4d3
app: add signature fitting migration, #TASK-2242
pfurio Nov 9, 2022
65edb26
app: set default fitting id to fitting-1, #TASK-2242
pfurio Nov 10, 2022
c7c7859
Change version to 2.5.0-SNAPSHOT after merge v2.4.10
juanfeSanahuja Nov 11, 2022
971883a
Prepare release 2.5.0
juanfeSanahuja Nov 11, 2022
480deb4
Prepare new development version 2.5.1-SNAPSHOT
juanfeSanahuja Nov 11, 2022
f7e22c0
Prepare new development version
juanfeSanahuja Nov 11, 2022
89bf7d3
Prepare 2.4.6-SNAPSHOT
juanfeSanahuja Nov 11, 2022
6be4b79
Prepare 2.6.0-SNAPSHOT
juanfeSanahuja Nov 11, 2022
43730b0
pom:Update java-common-libs and biodata versions
juanfeSanahuja Nov 11, 2022
0b1e035
analysis: compute counts for SV, #TASK-2242, #TASK-2353
jtarraga Nov 17, 2022
621def7
analysis: generate the catalogue.tsv file for SV variants, and add ju…
jtarraga Nov 18, 2022
970f979
analysis: add junit test for SV fitting, #TASK-2242, #TASK-2353
jtarraga Nov 21, 2022
88128fa
analysis: add file mutational-signature-sv.json for testing, #TASK-22…
jtarraga Nov 21, 2022
26a833d
Merge branch 'TASK-2242' of https://github.com/opencb/opencga into TA…
jtarraga Nov 21, 2022
979db49
analysis: add files for params, analysis and executor for the HRDetec…
jtarraga Nov 22, 2022
415f0bf
Resolve conflicts by updating package versions, #TASK-2242
jtarraga Nov 22, 2022
a01a904
analysis: fix compilation errors, #TASK-2274, #TASK-2369
jtarraga Nov 22, 2022
0c8f375
analysis: new HRDetect parameters, #TASK-2274, #TASK-2369
jtarraga Nov 22, 2022
20af5e1
update version script
juanfeSanahuja Nov 23, 2022
3eaaa52
update dependency script
juanfeSanahuja Nov 23, 2022
4256fea
analysis: mutational signature analysis job saves the results in samp…
jtarraga Nov 24, 2022
31371d9
analysis: rename translocation category name from 'tr' to 'trans', #T…
jtarraga Nov 24, 2022
d383599
update dependency script
juanfeSanahuja Nov 24, 2022
5c1c075
Update java-common-libs dependency to 4.6.0-TASK-2390-SNAPSHOT
juanfeSanahuja Nov 24, 2022
dc3a05a
Update java-common-libs dependency to 4.6.0-SNAPSHOT
juanfeSanahuja Nov 24, 2022
548cca2
update dependency script
juanfeSanahuja Nov 24, 2022
046149d
Update java-common-libs dependency to 4.6.0-TASK-2390-SNAPSHOT
juanfeSanahuja Nov 24, 2022
4dd5d18
Deleted update version script
juanfeSanahuja Nov 25, 2022
6c46c96
Update java-common-libs dependency to 4.6.0-SNAPSHOT
juanfeSanahuja Nov 25, 2022
3bc0488
analysis: improve junit tests for mutational signature, #TASK-2242, #…
jtarraga Nov 29, 2022
78d2c51
Merge branch 'TASK-2242' into TASK-2274
jtarraga Nov 29, 2022
6d174d8
catalog: fix test performance using mongo5, #TASK-2297
pfurio Nov 30, 2022
6ea107f
Minor code improvements
imedina Nov 30, 2022
0df246c
analysis: update according to biodata changes (HRDetec data model), u…
jtarraga Nov 30, 2022
17a2993
analysis: add bootstrap parameter to the junit test, #TASK-2274, #TAS…
jtarraga Dec 1, 2022
ac44ae1
analysis: implement CLI and web service for HRDetectAnalysis, #TASK-2…
jtarraga Dec 1, 2022
48b1812
catalog: fix several tests, #TASK-2297
pfurio Dec 2, 2022
1334675
catalog: fix all tests, #TASK-2297
pfurio Dec 5, 2022
ebd586f
analysis: fix some errors, #TASK-2242, #TASK-2353
jtarraga Dec 5, 2022
fde1c46
Merge branch 'TASK-2242' into TASK-2274
jtarraga Dec 5, 2022
3a986c0
Clean spaces
juanfeSanahuja Dec 12, 2022
6ce48dd
Merge branch 'TASK-2390' of https://github.com/opencb/opencga into TA…
juanfeSanahuja Dec 12, 2022
a564f12
Port Patch Version 1.2.11 #TASK-2474
juanfeSanahuja Dec 13, 2022
e59c6af
Port Patch Version 1.2.10.1 #TASK-2475
juanfeSanahuja Dec 13, 2022
beccef5
Merge and resolve conflicts, #TASK-2242
jtarraga Dec 19, 2022
f18172b
Resolve conflicts, #TASK-2274
jtarraga Dec 19, 2022
2c834d2
Port Patch Version 1.2.12 #TASK-2525
juanfeSanahuja Dec 22, 2022
6189163
analysis: fix some bugs and improve junit test, #TASK-2274, #TASK-2369
jtarraga Dec 26, 2022
13fd25d
Merge pull request #2222 from opencb/TASK-2297
pfurio Dec 27, 2022
74d985e
catalog: fix sample-individual association issue, #TASK-2539
pfurio Dec 27, 2022
f960658
core: fix Junit test
imedina Jan 4, 2023
224c6e8
catalog: stop using old MongoClient, #TASK-2297
pfurio Jan 4, 2023
557f99f
storage: remove opencga-storage-mongodb dependency, #TASK-2297
pfurio Jan 4, 2023
99cc311
Check if the branch name begin per TASK-
juanfeSanahuja Jan 5, 2023
fb62379
Rebuild autogenerated code and merge develop
juanfeSanahuja Jan 5, 2023
4087ef4
Merge pull request #2216 from opencb/TASK-2242
juanfeSanahuja Jan 5, 2023
30d5606
Minor improvements in the dependency synchonisator
imedina Jan 5, 2023
b0f75c6
misc: sync_dependency.sh refactor to method update_library #TASK-2390
juanfeSanahuja Jan 5, 2023
1f931af
Update 'java-common-libs.version' dependency to 4.6.0-TASK-2390-SNAPSHOT
juanfeSanahuja Jan 5, 2023
329602d
Update 'java-common-libs.version' dependency to 4.6.0-SNAPSHOT
juanfeSanahuja Jan 5, 2023
e613ec6
Merge branch 'develop' into TASK-2390
juanfeSanahuja Jan 5, 2023
74397e7
storage: Use dataRelease when calling to cellbase. #TASK-2575
j-coll Jan 6, 2023
a909a13
Resolve conflicts (after merging develop), #TASK-2274
jtarraga Jan 9, 2023
4514483
Merge branch 'TASK-2539' into develop
imedina Jan 9, 2023
2f1c2d4
Merge pull request #2226 from opencb/TASK-1201
j-coll Jan 9, 2023
602632c
Merge pull request #2225 from opencb/TASK-2390
juanfeSanahuja Jan 9, 2023
f99edea
Merge pull request #2217 from opencb/TASK-2274
jtarraga Jan 9, 2023
bc82ec4
JUnit minor fixes
imedina Jan 10, 2023
3621810
Resolve conflicts after merging develop, #TASK-2303
jtarraga Jan 10, 2023
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Merge branch 'release-2.4.x' into TASK-2242
@jtarraga
jtarraga committed Nov 8, 2022
commit abd38973c110f67e2b25887354f81a41a284f742

This merge commit was added into this branch cleanly.

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