TASK-5388 - Add AlphaMissense predictions #698
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… #TASK-5407, #TASK-5387
…e predictions, #TASK-5418, #TASK-5388
…K-5407, #TASK-5387
…ownloaded file, #TASK-5419, #TASK-5388
…TASK-5419, #TASK-5388
…and add suppor for loading AlphaMissense in that collection, #TASK-5420, #TASK-5388
…collection, #TASK-5420, #TASK-5388
…he new data model, #TASK-5442, #TASK-5388
…hen versions, #TASK-5442, #TASK-5388
…phen, revel and alphamissense), #TASK-5464, #TASK-5388
…tution predictions (sift, polyphen, revel and alphamissense), #TASK-TASK-5421, #TASK-5388
…and move the function to unzip PharmGKB files from the downloader to the builder, #TASK-5776, #TASK-5564
…sonnar issues, #TASK-5775, #TASK-5564
…rom a given data, #TASK-5775, #TASK-5564
… sonnar issues, #TAK-5776, #TASK-5564
…g code and fixing sonnar issues, #TASK-5776, #TASK-5564
…dd log messages, #TASK-5775, #TASK-5564
…cks and log messages, #TASK-5776, #TASK-5564
…-5775, #TASK-5564
…, #TASK-6142, #TASK-5564
…ASK-5776, #TASK-5564
…vements and sonnar fixes), #TASK-5776, #TASK-5564
Resolve conflicts: cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java And add exception to PgsDownloadManager.java
Resolve conflicts: cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ExportCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java cellbase-core/src/main/resources/configuration.yml cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/RevelScoreBuilder.java cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/AbstractDownloadManager.java cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/Downloader.java cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/RevelScoresDownloadManager.java cellbase-lib/src/main/resources/mongodb-indexes.json And update code according to the last changes.
…ilder, #TASK-5407, #TASK-5387
…ile to the build step, adding log messages, fixing sonnar issues,... #TASK-5575, #TASK-5564
…ile to the build step, adding checks and log messages, fixing sonnar issues,... #TASK-5576, #TASK-5564
Resolve conflicts: cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java
Resolve Conflicts: cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ExportCommandExecutor.java cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java cellbase-core/src/main/resources/configuration.yml cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
j-coll
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Add AlphaMissense predictions