You can find more detailed information at GitHub Issues.
1.4.2. contains a small series of internal changes requiring running a small migration. To do so, please head to the main OpenCGA source folder and run the following:
|
transcriptionFlag
" to "transcriptFlag
" (#1256)cohortStatsAlt
", "cohortStatsRef
" (#1239)[FEATURE] Aggregate operation for all samples from a study in the Variant (#757)
[IMPROVEMENT] Move HBase write step to a separated MR for fill-missing operation (#815)
[IMPROVEMENT] Mark already processed variants in fill missing operation (#803)
[IMPROVEMENT] Do not iterate over all VcfRecords when filling gaps or missing variants (#794)
[IMPROVEMENT] Fill missing prepare step: copy variants to fill into archive table (#793)
[IMPROVEMENT] Split VcfSlice from archive table in REF and NON_REF columns (#778)
[IMPROVEMENT] Split archive table in file batches (#777)
[CHANGE] Remove merge=advanced from storage-hadoop (#796)
[FEATURE] Index Sample Genotypes in HBase (#838)
[FEATURE] New Variant query filter "clinicalSignificance" (#872)
[FEATURE] Add filter by QUAL in Storage Variants (#809)
[FEATURE] Accept enriched genotypes at GENOTYPE filter (#750)
[FEATURE] Variant filtering in a samples group (#578)
[CHANGE] Automatic INCLUDE_STUDY if possible (#878)
[CHANGE] Automatic INCLUDE_SAMPLE if GENOTYPE VariantQueryParam is present (#814)
[IMPROVEMENT] Match Consequence type with the specified Gene filter (if any) for Storage Hadoop (#874)
[CHANGE] Untie internal Catalog and Storage IDs (#859)
[FIX] Synchronize Catalog ID to UID changes in Storage Managers catalog (#861)
[FEATURE] Create a ProjectMetadata object for Variant Storage (#832)
[IMPROVEMENT] Move storage-hadoop metadata to a separated table (#781)
[FEATURE] Support and load BREAKENDS in Variant Storage (#760)
[FEATURE] Support of Symbolic and Structural variants in Hadoop Variant Storage (#857)
[IMPROVEMENT] Add direct loader for the first file in a chromosome to load directly to the variants collection (#354)
[FEATURE] Move removed variants into a trash bin (#831)
[CHANGE] By default, load all FORMAT fields in Variant Storage MongoDB (#824)
[CHANGE] Change storage-hadoop table naming policy (#782)
[IMPROVEMENT] Review and improve Variant Annotation in OpenCGA Storage (#805)
[IMPROVEMENT] Create one Stage Collection per study in Variants Storage MongoDB (#801)
[IMPROVEMENT] Filter out overlapping files in variants in storage-hadoop (#779)
[IMPROVEMENT] Improve remove file in variant-storage-hadoop (#776)
[IMPROVEMENT] Load annotation using BufferedMutator (#775)
[FIX] Do not store phoenix primary key columns in HBase as separated columns (#802)
[FIX] Adapt remove file to new archive schema (#800)
[FIX] Do not map namespace for VIEW tables under phoenix 4.12.0 (#799)
[FIX] Avoid PhoenixIOException timeout when dropping columns from phoenix (#795)
OpenCGA storage hadoop is not available in this version. To compile use this line:
mvn clean install -DskipTests -pl '!:opencga-storage-hadoop-core'
This release constitutes the first release candidate (RC1). This is the biggest release ever with more than 1,400 commits, special mention to j-coll and pfurio for their contribution in Catalog, Storage and Server components.
Third Beta
Second Beta
First Beta
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