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Ticket Summary Owner Type Priority Milestone Component
#1016 Implement Stringtie step in the Hisat pipeline Nicklas Nordborg task major Reggie v4.15 net.sf.basedb.reggie
#1017 Remove code for handling optional MaskedSequences Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1018 Updates to HaplotypeCaller step Nicklas Nordborg enhancement major Reggie v4.15 net.sf.basedb.reggie
#1019 Secondary analysis wizards should sort items by library plate order Nicklas Nordborg enhancement major Reggie v4.15 net.sf.basedb.reggie
#1021 Add INCA 2.0 columns to the blacklist enhancement major INCA XML to CSV converter 1.2 net.sf.basedb.inca
#1022 INCA import/statistics wizards changes due to INCA 2.0 Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1023 Release exporter changes due to INCA 2.0 Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1024 Create annotation type definitions for INCA 2.0 Nicklas Nordborg task major Reggie v4.16 net.sf.basedb.reggie
#1025 Release exporter should support StringTie data Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1026 Create wizard for secondary analysis cleanup Nicklas Nordborg task major Reggie v4.16 net.sf.basedb.reggie
#1027 External samples and Stratagene should not be part of genotyping qc Nicklas Nordborg defect major Reggie v4.16 net.sf.basedb.reggie
#1028 Add support for StringTie data enhancement major Relax v1.2 net.sf.basedb.relax
#1030 The "Force update counters" icon on the Reggie start page feels unresponsive Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1031 Define a genotype QC flag that can be set on alignments that has been verified to match another sample Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1032 Reference date batch update wizard changes due to INCA 2.0 Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1034 Remove expression matrix from release exporter Nicklas Nordborg task major Reggie v4.16 net.sf.basedb.reggie
#1036 Add support for public/private key authentication enhancement major Open Grid Scheduler service v1.2 net.sf.basedb.opengrid
#1037 Depend on BASE 3.13 task major Open Grid Scheduler service v1.2 net.sf.basedb.opengrid
#1038 Add support for SSH connections with private key authentication Nicklas Nordborg task major External files support 1.4 net.sf.basedb.xfiles
#1041 The release exporter should export the QC_GenoTypeHET_PCT annotation Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1043 The Level 3 exporter fails if the release server has a specified port defect major Relax v1.2 net.sf.basedb.relax
#1044 Selecting INCA annotations for the Level 3 exporter enhancement major Relax v1.2 net.sf.basedb.relax
#1046 Flagged alignments wizard Nicklas Nordborg task major Reggie v4.17 net.sf.basedb.reggie
#1049 Improvments to the FrozenTissueDate wizards Nicklas Nordborg enhancement major Reggie v4.18 net.sf.basedb.reggie
#1050 More functionality in the Flagged alignment wizard Nicklas Nordborg enhancement major Reggie v4.18 net.sf.basedb.reggie
#1051 The Release exporter plug-in should assist when creating zip files with expression data Nicklas Nordborg enhancement major Reggie v4.18 net.sf.basedb.reggie
#1054 Even more functionality in the Flagged alignment wizard Nicklas Nordborg enhancement major Reggie v4.20 net.sf.basedb.reggie
#1055 Implement extension for logging in with OTP Nicklas Nordborg task major OTP login v1.0 net.sf.basedb.otp
#1057 Description on *.dil items is incorrect Nicklas Nordborg defect major Reggie v4.19 net.sf.basedb.reggie
#1062 OTP setup should not be allowed for multi-user accounts Nicklas Nordborg enhancement major OTP login v1.1 net.sf.basedb.otp
#1067 Highlight related items in Case summary Nicklas Nordborg enhancement major Reggie v4.20 net.sf.basedb.reggie
#1068 Add mBAF analysis step to the Hisat/StringTie pipeline Nicklas Nordborg task major Reggie v4.20 net.sf.basedb.reggie
#1070 The consent registration wizard doesn't check existing consent Nicklas Nordborg defect major Reggie v4.20 net.sf.basedb.reggie
#1071 Installation wizard doesn't show error message defect major Relax v1.4 net.sf.basedb.relax
#1072 Introduce Lysate item between RNA and Specimen Nicklas Nordborg Request major Relax v1.4 net.sf.basedb.relax
#1073 Switch to BASE 3.13 enhancement major Relax v1.4 net.sf.basedb.relax
#1074 Add more subtypes Nicklas Nordborg enhancement major Relax v1.4 not classified
#1075 Change the release exporter to work with list of patients Nicklas Nordborg task major Reggie v4.21 net.sf.basedb.reggie
#1076 The Level 3 export plug-in should generate rsync script with -L option defect major Relax v1.4 net.sf.basedb.relax
#1077 All biosource items should have an external id (release id) Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1078 "Not asked" subtype should be renamed to "NotAsked" Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1080 Add "Manual" option to the DoNotUse annotation type Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1081 The release exporter should export more data Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1084 DataFileFolder annotation should always set a default value enhancement major Relax v1.4 net.sf.basedb.relax
#1090 Introduce FirstReleasedIn annotation task major Relax v1.4 net.sf.basedb.relax
#1092 Detect configuration changes automatically Nicklas Nordborg enhancement major YubiKey v1.5 net.sf.basedb.yubikey
#1093 Detect configuration changes automatically Nicklas Nordborg enhancement major OTP login v1.2 net.sf.basedb.otp
#1094 The OTP field should not be locked to numbers Nicklas Nordborg enhancement major OTP login v1.2 net.sf.basedb.otp
#1095 Implement "update" mode for the release importer Nicklas Nordborg enhancement major Relax v1.4 net.sf.basedb.relax
#1096 The "Release importer" plug-in should be moved to project page enhancement major Relax v1.4 net.sf.basedb.relax
#1098 Release exporter should generate scripts that works with the "update" importer mode Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1099 The cohort exporter should have support for exporting downstream items Nicklas Nordborg task major Relax v1.4 net.sf.basedb.relax
#1100 The release exporter should set subtype on raw bioassay annotations Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1104 Re-factor the INCA import Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1108 Fix INCA statistics Nicklas Nordborg task major Reggie v4.22 not classified
#1109 INCA report files should be encrypted Nicklas Nordborg enhancement major Reggie v4.22 net.sf.basedb.reggie
#1110 Support for Excel files as an alternative to tab-separated files Nicklas Nordborg task major Reggie v4.22 net.sf.basedb.reggie
#1115 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major OTP login v1.3 net.sf.basedb.otp
#1116 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major YubiKey v1.6 net.sf.basedb.yubikey
#1117 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major Open Grid Scheduler service v1.3 net.sf.basedb.opengrid
#1118 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task major Relax v1.5 net.sf.basedb.relax
#1120 Remove Apache POI from distribution Nicklas Nordborg task major Reggie v4.23 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
#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
#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
#1126 Cohort exporter should support exporting to Excel file enhancement major Relax v1.5 net.sf.basedb.relax
#1128 Add support for svg images Nicklas Nordborg task major Thumbnails v1.1 net.sf.basedb.thumbnails
#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
#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
#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
#1139 TypeError: item is undefined in Flagged alignment wizard Nicklas Nordborg defect major Reggie v4.22.2 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
#1147 Switch to Java 11 and BASE 3.15 Nicklas Nordborg task major OTP login v1.3 net.sf.basedb.otp
#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
#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
#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
#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
#1156 Switch to Java 11 and BASE 3.15 olle task major LabEnv v1.7 net.sf.basedb.labenv
#1159 Release exporter changes due to MIPs pipeline Nicklas Nordborg enhancement major 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
#1164 Pipeline annotation in secondary analysis Nicklas Nordborg enhancement major Reggie v4.23 net.sf.basedb.reggie
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