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Ticket Summary Owner Type Priority Milestone Component
#1111 Changes in the INCA import Nicklas Nordborg enhancement minor Reggie v4.22 net.sf.basedb.reggie
#1112 Add a predefined option in the referral form registration when a case is registered without referral form Nicklas Nordborg enhancement minor Reggie v4.22 net.sf.basedb.reggie
#1113 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task minor Reggie v4.22 net.sf.basedb.reggie
#1121 Map external data to releases should encrypt the temporary file Nicklas Nordborg enhancement major Reggie v4.22 net.sf.basedb.reggie
#1122 Map external data to releases should not include case or specimen external id Nicklas Nordborg task major Reggie v4.22 net.sf.basedb.reggie
#1124 Pause specimen after registration Nicklas Nordborg task major Reggie v4.22 net.sf.basedb.reggie
#1125 Unpause a paused specimen Nicklas Nordborg task major Reggie v4.22 net.sf.basedb.reggie
#1127 Thumbnails are not visible in BASE 3.15 Nicklas Nordborg task blocker Thumbnails v1.1 net.sf.basedb.thumbnails
#1128 Add support for svg images Nicklas Nordborg task major Thumbnails v1.1 net.sf.basedb.thumbnails
#1132 Reggie fails to create lab protocol for allprep isolation in BASE 3.15 Nicklas Nordborg defect major Reggie v4.22.1 net.sf.basedb.reggie
#1139 TypeError: item is undefined in Flagged alignment wizard Nicklas Nordborg defect major Reggie v4.22.2 net.sf.basedb.reggie
#1150 Switch to Java 11 and BASE 3.15 Nicklas Nordborg task major External files support 1.5 net.sf.basedb.xfiles
#1151 Update SSH library Nicklas Nordborg task major External files support 1.5 net.sf.basedb.xfiles
#1114 Remove null="false" from "otp_requried" column definition Nicklas Nordborg defect minor OTP login v1.3 net.sf.basedb.otp
#1115 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major OTP login v1.3 net.sf.basedb.otp
#1147 Switch to Java 11 and BASE 3.15 Nicklas Nordborg task major OTP login v1.3 net.sf.basedb.otp
#1117 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major Open Grid Scheduler service v1.3 net.sf.basedb.opengrid
#1152 Switch to Java 11 and BASE 3.15 Jari Häkkinen task major Open Grid Scheduler service v1.3 net.sf.basedb.opengrid
#1153 Update SSH library Nicklas Nordborg task major Open Grid Scheduler service v1.3 net.sf.basedb.opengrid
#1116 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major YubiKey v1.6 net.sf.basedb.yubikey
#1148 Switch to Java 11 and BASE 3.15 Nicklas Nordborg task major YubiKey v1.6 net.sf.basedb.yubikey
#1149 Update Yubico client API Nicklas Nordborg task major YubiKey v1.6 net.sf.basedb.yubikey
#1118 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major Relax v1.5 net.sf.basedb.relax
#1123 Map external data to releases should not include case or specimen external id Nicklas Nordborg enhancement major Relax v1.5 net.sf.basedb.relax
#1126 Cohort exporter should support exporting to Excel file enhancement major Relax v1.5 net.sf.basedb.relax
#1154 Switch to Java 11 and BASE 3.15 Nicklas Nordborg task major Relax v1.5 net.sf.basedb.relax
#1155 Map external data to releases should encrypt the temporary file Nicklas Nordborg enhancement major Relax v1.5 net.sf.basedb.relax
#1168 Safer debugging of import/export plug-in Nicklas Nordborg enhancement major Relax v1.5 net.sf.basedb.relax
#1119 Re-implement TIFF to JPG conversion for Histology images using the ImageIO API Nicklas Nordborg enhancement critical Reggie v4.23 net.sf.basedb.reggie
#1120 Remove Apache POI from distribution Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1129 DNA pre-normalization Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1130 Import wizard for MIPs aliquot plates Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1131 Switch to BASE 3.15 Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1133 Re-organize the Reggie front page Nicklas Nordborg enhancement critical Reggie v4.23 net.sf.basedb.reggie
#1134 Implement an "Activity log" Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1135 Design MIPs plate wizard Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1136 MIPs plate lab protocol Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1137 Register MIPs libraries Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1138 MIPs pooling Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1140 Switch to Java 11 Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
#1141 Improve error message when an item is registred in duplicate Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
#1142 Create MIPs flow cell and start/end/confirm sequencing Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1143 INCA import fails if the last column is empty in one or more rows Nicklas Nordborg defect major Reggie v4.23 net.sf.basedb.reggie
#1144 Line numbers in the INCA report files seems to be data lines and not file lines Nicklas Nordborg defect major Reggie v4.23 net.sf.basedb.reggie
#1145 Location of data for external RNA Nicklas Nordborg defect major Reggie v4.23 net.sf.basedb.reggie
#1146 Demux for the MIPs pipeline Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1157 Case summary changes due to MIPs pipeline Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1158 FASTQ files for external samples should not have the prefix in their names Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1159 Release exporter changes due to MIPs pipeline Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
#1160 Investigate changes in Picard since our last modified version Nicklas Nordborg task critical Reggie v4.23 net.sf.basedb.reggie
#1161 Update picard to 2.20 Nicklas Nordborg task major Reggie v4.23 net.sf.basedb.reggie
#1162 Add support for using 'M' in the read-string when demuxing Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
#1163 Start demux wizard may display the same sequencing run multiple times if it is marked for re-process Nicklas Nordborg defect minor Reggie v4.23 net.sf.basedb.reggie
#1164 Pipeline annotation in secondary analysis Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
#1165 Code for checking if a sample is external or not is incorrect Nicklas Nordborg defect major Reggie v4.23 net.sf.basedb.reggie
#1166 Add configuration setting for disabling counting stray folders Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1167 Safer debugging of release exporter plug-in Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1169 The private-key file of a file-server is ignored in the installation servlet Nicklas Nordborg defect minor Reggie v4.23 net.sf.basedb.reggie
#1171 Hisat alignment stops without error if the genotype VCF file can't be parsed Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1172 The message in the "Secondary analysis cleanup" wizard is confusing Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1173 Link a single <host> entry to more than one OpenGrid cluster Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1174 Permission on files created by secondary analysis for external samples Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1175 Temporary R working files may be left in open state Nicklas Nordborg defect trivial Reggie v4.23 net.sf.basedb.reggie
#1176 The keep-session-alive functionality should not hide current messages Nicklas Nordborg defect minor Reggie v4.23 net.sf.basedb.reggie
#1177 Remove <add-read-groups-options> from reggie-config.xml Nicklas Nordborg Request trivial Reggie v4.23.1 net.sf.basedb.reggie
#1178 Scripts should not fail if it can't change group on files Nicklas Nordborg enhancement major Reggie v4.23.1 net.sf.basedb.reggie
#1179 The "Number of slots" value in the Start demux wizard is always from the <demux> configuration Nicklas Nordborg defect major Reggie v4.23.1 net.sf.basedb.reggie
#1180 Activity log entry for "sequencing ended" should be registered by "Auto-confirm" user Nicklas Nordborg defect trivial Reggie v4.23.1 net.sf.basedb.reggie
#1181 Incorrect counter for pilot reports in the activity log Nicklas Nordborg defect major Reggie v4.23.1 net.sf.basedb.reggie
#1182 Activity log entry for "pilot reports" should be registered by "Auto-confirm" user Nicklas Nordborg defect trivial Reggie v4.23.1 net.sf.basedb.reggie
#1183 Change to picard 2.20.8 or later Nicklas Nordborg enhancement major Reggie v4.23.1 net.sf.basedb.reggie
#1184 Increase the number of entries displayed by the activity log Nicklas Nordborg enhancement major Reggie v4.23.1 net.sf.basedb.reggie
#1185 Add link to the demultiplex metrics file in the "Confirm demux" wizards Nicklas Nordborg enhancement minor Reggie v4.23.1 net.sf.basedb.reggie
#1191 Remove debug output from GenotypeMessage Nicklas Nordborg defect trivial Reggie v4.23.2 net.sf.basedb.reggie
#1192 The "Flag RNA" option should not be checked by default in legacy pipeline for failed jobs Nicklas Nordborg defect minor Reggie v4.23.2 net.sf.basedb.reggie
#1193 The "Map external data to releases" wizard should have more options Nicklas Nordborg enhancement major Reggie v4.23.2 net.sf.basedb.reggie
#1194 Import more data from MIPs file Nicklas Nordborg enhancement critical Reggie v4.23.2 net.sf.basedb.reggie
#1195 The "Map external data to releases" wizard should have an option to re-order output file Nicklas Nordborg enhancement minor Reggie v4.23.2 net.sf.basedb.reggie
#1187 Implement an "External RNA import" wizard Nicklas Nordborg task major Reggie v4.24 net.sf.basedb.reggie
#1188 Register destruction of stored samples and extracts in the "Retraction wizard" Nicklas Nordborg enhancement major Reggie v4.24 net.sf.basedb.reggie
#1189 The retraction destruction wizard try to connect to the file server even if there are no files to delete Nicklas Nordborg defect trivial Reggie v4.24 net.sf.basedb.reggie
#1196 Incorrect specifications in the mRNA protocol Nicklas Nordborg defect critical Reggie v4.24 net.sf.basedb.reggie
#1197 Rounding effects may cause the mRNA protocol to incorrectly display "Large mix" Nicklas Nordborg defect trivial Reggie v4.24 net.sf.basedb.reggie
#1198 Add support for PAD to the "Map external data" wizard Nicklas Nordborg enhancement major Reggie v4.24 net.sf.basedb.reggie
#1199 Implement Variant calling pipeline Nicklas Nordborg task major Reggie v4.24 net.sf.basedb.reggie
#1201 Incorrect date is displayed for variant calling in the case summary Nicklas Nordborg defect minor Reggie v4.24.1 net.sf.basedb.reggie
#1202 Add check for duplicate barcode template in the MIPs library registration Nicklas Nordborg enhancement major Reggie v4.24.1 net.sf.basedb.reggie
#1203 Resolve thread deadlocks Nicklas Nordborg defect minor Reggie v4.24.1 net.sf.basedb.reggie
#1204 Change default flow cell type in MIPs create flow cells wizard Nicklas Nordborg enhancement major Reggie v4.24.1 net.sf.basedb.reggie
#1205 Variant calling fails with "malformed BED entry" Nicklas Nordborg defect major Reggie v4.24.1 net.sf.basedb.reggie
#1206 The MIPs aliquot importer should handle some values as special cases Nicklas Nordborg enhancement minor Reggie v4.24.1 net.sf.basedb.reggie
#1207 Replace the "Nothing yet" in the activity log with a quote-of-the-day Nicklas Nordborg enhancement minor Reggie v4.25 net.sf.basedb.reggie
#1208 Implement wizard for building database of variant frequencies in SCAN-B samples Nicklas Nordborg task major Reggie v4.25 net.sf.basedb.reggie
#1209 Add support for storing TMA specimen Nicklas Nordborg task major Reggie v4.25 net.sf.basedb.reggie
#1210 Variant calling fails if no variants are found Nicklas Nordborg defect minor Reggie v4.25 net.sf.basedb.reggie
#1212 Enable filtering step for variant calling in auto-confirm mode Nicklas Nordborg enhancement minor Reggie v4.25 net.sf.basedb.reggie
#1213 Firefox fails to open some Print dialogs Nicklas Nordborg defect minor Reggie v4.25 net.sf.basedb.reggie
#1214 Add support for external specimen Nicklas Nordborg task major Reggie v4.25 net.sf.basedb.reggie
#1215 Include mutation signature analysis in the variant calling pipeline Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1216 Finalize the "Confirm MIPs demux" wizard Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
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