v2.4.7

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

v2.4.6

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

v2.2.8

What's Changed

• TASK-2111 by @pfurio in #2156

Full Changelog: v2.2.7...v2.2.8

v2.2.7

What's Changed

• TASK-2111: "and" queries are not working in RGA by @pfurio in #2148

Full Changelog: v2.2.6...v2.2.7

v2.2.6

What's Changed

• TASK-2033 by @pfurio in #2136 #2138

Full Changelog: v2.2.5...v2.2.6

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

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

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

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

v2.3.3

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

Full Changelog: v2.3.2...v2.3.3