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Ticket Summary Owner Type Priority Milestone Component
#1165 Code for checking if a sample is external or not is incorrect Nicklas Nordborg defect major Reggie v4.23 net.sf.basedb.reggie
#1168 Safer debugging of import/export plug-in Nicklas Nordborg enhancement major Relax v1.5 net.sf.basedb.relax
#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
#1181 Incorrect counter for pilot reports in the activity log Nicklas Nordborg defect major 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
#1186 Implement plug-in for running Single Sample Predictor models Nicklas Nordborg task major Reggie v4.27 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
#1193 The "Map external data to releases" wizard should have more options Nicklas Nordborg enhancement major Reggie v4.23.2 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
#1202 Add check for duplicate barcode template in the MIPs library registration Nicklas Nordborg enhancement major 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
#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
#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
#1219 Start demux wizard for MIPs should be a separate wizard Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1220 Auto-analyze in the MIPs pipeline should start the demux Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1222 Remove the G5 distance calculations from the variant calling script Nicklas Nordborg enhancement major Reggie v4.25 net.sf.basedb.reggie
#1224 The RNAseq library preperation wizard display protocols from other pipelines Nicklas Nordborg defect major Reggie v4.25 net.sf.basedb.reggie
#1228 Add file actions for viewing genotype and variant information Nicklas Nordborg enhancement major Reggie v4.26 net.sf.basedb.reggie
#1229 Import some variants as annotations Nicklas Nordborg enhancement major Reggie v4.26 net.sf.basedb.reggie
#1230 NullPointerException in the "Map external data" wizard Nicklas Nordborg defect major Reggie v4.25.1 net.sf.basedb.reggie
#1231 Add support for sequencing with NovaSeq Nicklas Nordborg task major Reggie v4.26 net.sf.basedb.reggie
#1234 Implement batch importer for followup blood samples Nicklas Nordborg task major Reggie v4.27 net.sf.basedb.reggie
#1239 Include Single Sample Predictor models in the StringTie pipeline Nicklas Nordborg task major Reggie v4.27 net.sf.basedb.reggie
#1240 Release exporter changes due to SSP Nicklas Nordborg enhancement major Reggie v4.27 net.sf.basedb.reggie
#1241 Some folders for external samples are not changed to the specified group Nicklas Nordborg defect major Reggie v4.27 net.sf.basedb.reggie
#1242 The Register external sequencing wizard should not auto-select the 4 lanes option Nicklas Nordborg defect major Reggie v4.27 net.sf.basedb.reggie
#1243 Improve status checking for NovaSeq Nicklas Nordborg defect major Reggie v4.27 net.sf.basedb.reggie
#1245 Picard demux should output compressed fastq files Nicklas Nordborg task major Reggie v4.27 net.sf.basedb.reggie
#1246 Race condition when displaying progress message Nicklas Nordborg defect major Reggie v4.27.1 net.sf.basedb.reggie
#1247 Add more translations to SSP plug-in Nicklas Nordborg enhancement major Reggie v4.27.1 net.sf.basedb.reggie
#1249 The temporary item list for importing variant call annotations is no longer needed Nicklas Nordborg task major Reggie v4.27.1 net.sf.basedb.reggie
#1250 The installation wizard should check/install annotation types needed for SSP Nicklas Nordborg enhancement major Reggie v4.27.1 net.sf.basedb.reggie
#1251 Add a mode to SSP plugin that run models for all rawbioassays with no value Nicklas Nordborg enhancement major Reggie v4.27.1 net.sf.basedb.reggie
#1253 Change the name in VCF file created by variant calling Nicklas Nordborg defect major Reggie v4.27.2 net.sf.basedb.reggie
#1255 The "Forwarded" option/date in the Retraction wizard should be removed Nicklas Nordborg enhancement major Reggie v4.27.3 net.sf.basedb.relax
#1256 Laterality annotations should be marked as "project-specific" by the release exporter Nicklas Nordborg enhancement major Reggie v4.27.3 net.sf.basedb.reggie
#1257 Remove the one-time-fix implemented for inserting lysate items between specimen and RNA Nicklas Nordborg task major Relax v1.6 net.sf.basedb.relax
#1258 Listing of clusters fails if one host can't be reached Nicklas Nordborg defect major Job scheduler extension v1.4 net.sf.basedb.opengrid
#1260 Demux started via auto-confirm should include items with DoNotUse flag Nicklas Nordborg defect major Reggie v4.27.4 net.sf.basedb.reggie
#1261 Switch to BASE 3.17 Nicklas Nordborg enhancement major Job scheduler extension v1.4 net.sf.basedb.opengrid
#1262 Upgrade ssh library Nicklas Nordborg enhancement major Job scheduler extension v1.4 net.sf.basedb.opengrid
#1265 Export more information in the release exporter Nicklas Nordborg enhancement major Reggie v4.27.4 net.sf.basedb.reggie
#1266 Run prepDE.py in the StringTie pipeline Nicklas Nordborg task major Reggie v4.27.4 net.sf.basedb.reggie
#1269 Timeout while searching for existing files in the Release exporter Nicklas Nordborg enhancement major Reggie v4.28 net.sf.basedb.reggie
#1270 Add support for pasting images to the Histology scoring wizard Nicklas Nordborg enhancement major Reggie v4.28 net.sf.basedb.reggie
#1271 HE glass images in the Histology wizard Nicklas Nordborg enhancement major Reggie v4.28 net.sf.basedb.reggie
#1273 Switch to java 11 and BASE 3.17 Nicklas Nordborg enhancement major Thumbnails v1.2 net.sf.basedb.thumbnails
#1274 Add support for NDPI images Nicklas Nordborg task major Thumbnails v1.2 net.sf.basedb.thumbnails
#1275 Implement support for rotating thumbnail images Nicklas Nordborg enhancement major Thumbnails v1.2 net.sf.basedb.thumbnails
#1276 Add more thumbnail sizes Nicklas Nordborg enhancement major Thumbnails v1.2 net.sf.basedb.thumbnails
#1277 Update to iText PDF 7 Nicklas Nordborg enhancement major Reggie v4.28 net.sf.basedb.reggie
#1279 Switch to BASE 3.17 Nicklas Nordborg enhancement major Reggie v4.28 net.sf.basedb.reggie
#1283 Missing translation for Biomek TruSeq mRNA library protocol Nicklas Nordborg defect major Reggie v4.29 net.sf.basedb.reggie
#1284 Add link to SCAN-B report in Case summary Nicklas Nordborg enhancement major Reggie v4.29 net.sf.basedb.reggie
#1285 Personal information on the SCAN-B report Nicklas Nordborg enhancement major Reggie v4.29 net.sf.basedb.reggie
#1286 Problems with the SCAN-B report when exporting with personal information Nicklas Nordborg enhancement major Reggie v4.30 net.sf.basedb.reggie
#1287 LinkedCase annotation Nicklas Nordborg enhancement major Reggie v4.30 net.sf.basedb.reggie
#1 Reformat plug-ins archive/download page to look like the rest of the trac environment. Jari Häkkinen task minor tracpages
#17 Export RMA bioassayset as a tab delimited file Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#28 Create plot observed/expected Johan Enell enhancement minor se.lu.onk.ztest
#29 Create plot FDR vs rank Johan Enell enhancement minor se.lu.onk.ztest
#30 Create combination plot Johan Enell enhancement minor se.lu.onk.ztest
#32 Create histogram plot Johan Enell enhancement minor se.lu.onk.ztest
#42 Add sample extended-properties.xml and configuration files needed for BASE plug-ins. Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#46 RMAExpress wiki page Peter Johansson task minor tracpages
#59 --with-gsl configure option Peter Johansson task minor se.lu.thep.wenni
#64 configure does not find basefile.h Jari Häkkinen defect minor se.lu.thep.wenni 0.7 se.lu.thep.wenni
#65 version number in BASE1 plugin is not updated automatically Peter Johansson enhancement minor se.lu.thep.wenni
#72 NNIFileConverter should not be installed in base2 mode Peter Johansson task minor se.lu.thep.wenni
#140 Add support in build.xml for automatic download of BASE jar files Nicklas Nordborg enhancement minor Illumina package v1.2 net.sf.basedb.illumina
#150 Fix layout of DetectionPValue.java Nicklas Nordborg task minor Illumina package v1.2 net.sf.basedb.illumina
#198 Change source files to UTF-8 Nicklas Nordborg task minor Extension examples v1.1 net.sf.basedb.examples.extensions
#199 Change source files to UTF-8 Nicklas Nordborg task minor Plugin examples v2.x net.sf.basedb.examples.plugins
#200 Change source files to UTF-8 Nicklas Nordborg task minor Web services examples v3.0 net.sf.basedb.examples.webservices
#201 Change source files to UTF-8 Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#202 Change source files to UTF-8 Nicklas Nordborg task minor Illumina package v1.4 net.sf.basedb.illumina
#203 Change source files to UTF-8 Nicklas Nordborg task minor MEV Launcher v1.3 net.sf.basedb.mev
#272 Handle CWD . commands correctly Nicklas Nordborg enhancement minor FTP Server v1.1 net.sf.basedb.ftp
#275 Version should autopropagate from build.xml Nicklas Nordborg task minor MeV Launcher v1.7 net.sf.basedb.mev
#276 Version should autopropagate from build.xml Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#283 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor Example code v1.3 net.sf.basedb.examples.extensions
#284 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor FTP Server v1.2 net.sf.basedb.ftp
#285 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor Illumina package v1.7 net.sf.basedb.illumina
#286 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor MeV Launcher v1.8 net.sf.basedb.mev
#288 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor Web services examples v3.0 net.sf.basedb.examples.webservices
#289 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Plugin examples v2.x net.sf.basedb.examples.plugins
#290 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Web services examples v3.0 net.sf.basedb.examples.webservices
#297 VirtualArray should activate "average on reporter" setting Jari Häkkinen defect minor VirtualArray 1.2 se.lu.onk series plug-ins
#298 VirtualArray can work with 1-channel data Jari Häkkinen enhancement minor VirtualArray 1.2 se.lu.onk series plug-ins
#301 Make sure installation instructions for VirtualArray are correct Jari Häkkinen defect minor VirtualArray 1.2 se.lu.onk series plug-ins
#351 Check case name in all wizards Nicklas Nordborg enhancement minor Reggie v2.2 net.sf.basedb.reggie
#356 Warning message about non-standard personal number is not shown when <enter> is used Nicklas Nordborg defect minor Reggie v2.3 net.sf.basedb.reggie
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