Releases: opencb/opencga
Releases · opencb/opencga
v2.4.8
8ad1038
This commit was signed with the committer’s verified signature.
juanfeSanahuja
Juanfe Sanahuja
Contributors
jtarraga, pfurio, and j-coll
Assets 4
v2.4.7
17f75fb
This commit was signed with the committer’s verified signature.
juanfeSanahuja
Juanfe Sanahuja
What's Changed
- TASK-2156 - Migration issues from 2.4.2 by @pfurio in #2161
- TASK-2080 - Exception in variant-export-run (parquet) chmod: changing permissions by @j-coll in #2145
- TASK-2152 - Missing important info in the Exomiser interpretation results by @jtarraga in #2163
Full Changelog: v2.4.6...v2.4.7
Contributors
jtarraga, pfurio, and j-coll
Assets 4
v2.4.6
b827cb6
This commit was signed with the committer’s verified signature.
juanfeSanahuja
Juanfe Sanahuja
What's Changed
- TASK-1705 - Update the fitting method in the signature analysis by @jtarraga in #2140
- TASK-2047 - Change ids to empty strings should not be allowed by @pfurio in #2141
- TASK-2063 - Can create individual and family without id by @pfurio in #2142
- TASK-2034 - Unable to find mate of variant by @j-coll in #2143
- TASK-2103 - Fail to load obsolete "actionable variants" file by @jtarraga in #2149
- TASK-2041 - Add HGVS data to consequenceTypes by @jtarraga in #2150
- TASK-2041 - Add HGVS data to consequenceTypes by @j-coll in #2151
- TASK-2075 - Support distinct by multiple fields by @pfurio in #2139
- TASK-1573 - Show FUSION in Role In Cancer column by @jtarraga in #2144
- TASK-2112 - Variant export sample will include only variants with clinical information by @j-coll in #2152
- TASK-2138 - Error creating opencga-internal.sh command line from nested job params by @j-coll in #2155
- TASK-1943 - Fix interpretation-exomiser analysis: too many variants by @jtarraga in #2157
- TASK-1289 - Improve CLI info error message by @juanfeSanahuja in #2154
Full Changelog: v2.4.5...v2.4.6
Contributors
jtarraga, pfurio, and 2 other contributors
Assets 3
v2.2.8
v2.2.7
v2.2.6
Contributors
pfurio
Assets 2
v2.4.5
What's Changed
- TASK-1904 - Array of files in job contains nulls by @pfurio in #2125
- TASK-1931 - RestApiParser does not consider fields of type 'double' and 'float' as primitives by @juanfeSanahuja in #2126
- TASK-1943 - Fix interpretation-exomiser analysis: too many variants by @jtarraga in #2129
- TASK-1934 - Default value is ignored in CLI generation process by @juanfeSanahuja in #2127
- TASK-1891 - Variant Browser: NumberFormatException: For input string: "" by @j-coll in #2128
- TASK-1935 - IllegalStateException error observed in the Sample Variant Browser when filtering by the PRAMEF6 gene by @j-coll in #2130
- TASK-1981 - RGA: Cannot filter by population frequency >= 0 by @pfurio in #2131
- TASK-1938 - Group by status in Case Portal in MSG is returning the wrong number of cases and a duplicated status group for NO_STATUS by @pfurio in #2132
- TASK-2011 - Export-run parquet by @j-coll in #2134
- TASK-1336 - DeNovo filter returns extra variants by @j-coll in #2133
- TASK-2017 - Queries with deleted doesn't work by @pfurio in #2135
- TASK-1812 - CLI 2.4.2-SNAPSHOT: families create ERROR and params naming by @juanfeSanahuja in #2119
- TASK-1296 - Parents should be a flag by @juanfeSanahuja in #2137
- TASK-1718 - Families distinct end-point fails in the REST API for field disorders.name by @juanfeSanahuja in #2118
Full Changelog: v2.4.4...v2.4.5
Contributors
jtarraga, pfurio, and 2 other contributors
Assets 3
v2.4.4
What's Changed
- TASK-1788 - Variant secondary sample index - family index fails "Undefined family trios" by @j-coll in #2109
- TASK-1795 - NPE from genes without name by @j-coll in #2110
- TASK-1480 - Wrong count of expected loaded variants by @j-coll in #2112
- TASK-633 - Variant query error when filtering by segregation - Operation Aggregated Family by @j-coll in #2111
- TASK-1789 - Fix interpretation Exomiser analysis when annotating primary findings by @jtarraga in #2114
- TASK-1773 - Fix individual quality control analysis by @jtarraga in #2113
- TASK-1214 - Enable automatic Zetta Test deployment by @j-coll in #2115
- TASK-1843 - Fix interpretation-tiering analysis when computing secondary findings by @jtarraga in #2116
- TASK-1856 - Relatedness analysis fails when the parameter 'minor allele frequency' is missing by @jtarraga in #2117
- TASK-1849 - Annotation id 'RNase_MRP_RNA' and Annotation id 'primary_transcript' is not an accepted key in the variable 'biotypeCount' by @pfurio in #2120
- TASK-1877 - java.lang.IllegalArgumentException: Unknown output format PARQUET_GZ by @j-coll in #2121
- TASK-1895 - Permission denied executing docker container at jobs in EMR by @j-coll in #2122
- TASK-696 - Case portal column Proband/sample, fail to show the sample when several rows with same proband use different samples by @pfurio in #2123
- TASK-1903 - Family members cannot be updated by @pfurio in #2124
Full Changelog: v2.4.3...v2.4.4
Contributors
jtarraga, pfurio, and j-coll
Assets 4
v2.4.3
What's Changed
- TASK-1593 - Variant-export-run : opencga-internal unknown parameter '--compress' by @j-coll in #2071
- TASK-1587 - The parameters of the body give an error by @juanfeSanahuja in #2068
- TASK-1519 - Variant Export in different output formats fails by @j-coll in #2072
- TASK-1120 - Errors in model MetaWS when class not found by @imedina in #2077
- TASK-1189 - Logout on expired session by @juanfeSanahuja in #2074
- TASK-1431 - CLi: error when using --host param by @juanfeSanahuja in #2075
- TASK-1487 - CLI: "Server Not Found" hidden by "Incorrect user or password" by @juanfeSanahuja in #2076
- TASK-563 - CLI: WS under the admin section are not in opencga.sh nor opencga-admin.sh by @juanfeSanahuja in #2067
- TASK-1280 - Port Patch Version 1.1.3 by @j-coll in #2082
- TASK-1254 - Cannot run program "hadoop-ssh.sh" Permission denied by @j-coll in #2065
- TASK-1194 - Add new fields to Catalog data model by @pfurio in #2079
- TASK-1386 - Shorten catalog indexed field variables by @pfurio in #2080
- TASK-1285 - Fix acl behaviour by @pfurio in #2083
- TASK-1664 - Error during migration of TASK-1470 by @pfurio in #2078
- TASK-1706 - NPE in variant export while avro serialization by @j-coll in #2085
- TASK-1708 - Variant export TPED fails if no output file name is provided by @j-coll in #2086
- TASK-1711 - Variant Export PARQUET wrong generated file by @j-coll in #2087
- TASK-1274 - VariantQueryException: Cannot Export VCF - Missing gene regions by @j-coll in #2088
- TASK-1713 - Variant Export using MR when should be using iterator on small queries by @j-coll in #2089
- TASK-1715 - Missing PopulationFrequency filters at VariantFilterBuilder by @j-coll in #2090
- TASK-1732 - Variant Export skips MapReduce for long queries using sample index by @j-coll in #2095
- TASK-1726 - Job aborted without enough error details by @j-coll in #2093
- TASK-1734 - Variant export MapReduce is filling the worker node disk by @j-coll in #2092
- TASK-1735 - Variant export : Sample 'mySample:1/1' not found by @j-coll in #2094
- TASK-1746 - Variant query/export from sample index with covered queries does not need variants table intersection by @j-coll in #2096
- TASK-1722 - Fix internal interpreter CLI name by @imedina in #2091
- TASK-1752 - Filter by chromosome-Linked segregation doesn't filter by chromosome by @j-coll in #2100
- TASK-1751 - Error during migration of TASK-1664 by @pfurio in #2098
- TASK-1756 - Variant export ClassCastException: java.lang.Double cannot be cast to java.lang.Float by @j-coll in #2102
- TASK-1537 - Fix the Exomiser wrapper analysis: it fails when multiple studies exist by @jtarraga in #2101
- TASK-1750 - Fix RGA performance issues by @pfurio in #2097
- TASK-1751 - Error during migration of TASK-1664 by @pfurio in #2103
- TASK-1481 - Fix the alignment command: coverage-index-run by @jtarraga in #2104
- TASK-1576 - Fix the inferred sex analysis: the karyotypic sex inferred is missing by @jtarraga in #2105
- TASK-1760 - Fix exomiser interpretation analysis by @jtarraga in #2106
- TASK-1497 - Fix the variant command: relatedness-run by @jtarraga in #2107
- TASK-1763 - Filter by chromosome-linked segregation at "sample" param. Defect of TASK-1752 by @j-coll in #2108
Full Changelog: v2.4.2...v2.4.3
Contributors
jtarraga, imedina, and 3 other contributors
Assets 4
v2.4.2
What's Changed
- TASK-1082 - CLI: Remove Collection parameters except primitive and string type lists by @juanfeSanahuja in #2066
- TASK-1472 - Review variant discussions don't show who and when were written by @pfurio in #2070
- TASK-1470 - Error in IVA Case explorer when searching by sample id by @pfurio in #2069
- TASK-1387 - Undesired behaviour in link-run operation by @pfurio in #2073
Full Changelog: v2.4.1...v2.4.2
Contributors
pfurio and juanfeSanahuja