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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
#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
#1020 Change novel-splicesite-outfile parameter to Hisat Nicklas Nordborg enhancement minor Reggie v4.15 net.sf.basedb.reggie
#973 Update to Hibernate 5.2 and BASE 3.12 olle task blocker LabEnv v1.6 net.sf.basedb.labenv
#974 A project should not be required olle task major LabEnv v1.6 net.sf.basedb.labenv
#975 Clean up unused javascript code olle task major LabEnv v1.6 net.sf.basedb.labenv
#976 Running 'ant update-version' doesn't update the version number in labenv.js olle defect major LabEnv v1.6 net.sf.basedb.labenv
#977 Re-design the Lab-sensor info page olle enhancement major LabEnv v1.6 net.sf.basedb.labenv
#978 Re-design the Lab sensor alarms page olle enhancement major LabEnv v1.6 net.sf.basedb.labenv
#1017 Remove code for handling optional MaskedSequences Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#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
#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
#1033 The INCA export wizard should only export personal numbers Nicklas Nordborg enhancement minor 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
#1040 Set max BASE version to 3.13 Nicklas Nordborg task minor Reggie v4.16 net.sf.basedb.reggie
#1041 The release exporter should export the QC_GenoTypeHET_PCT annotation Nicklas Nordborg enhancement major Reggie v4.16 net.sf.basedb.reggie
#1042 The release exporter fails if the release server has a specified port Nicklas Nordborg defect minor Reggie v4.16 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
#1028 Add support for StringTie data enhancement major Relax v1.2 net.sf.basedb.relax
#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
#1045 Display FrozenTissueDate annotation in case summary Nicklas Nordborg enhancement minor Reggie v4.17 net.sf.basedb.reggie
#1046 Flagged alignments wizard Nicklas Nordborg task major Reggie v4.17 net.sf.basedb.reggie
#1047 HaplotypeCaller should be wrapped with stdwrap.sh Nicklas Nordborg enhancement minor Reggie v4.18 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
#1052 The FrozenTissueDate importer fails if ProvID is the first or last column Nicklas Nordborg defect minor Reggie v4.18 net.sf.basedb.reggie
#1053 The "High HET" filter in the "Flagged alignments" wizard should load more alignments Nicklas Nordborg defect critical Reggie v4.18 net.sf.basedb.reggie
#1038 Add support for SSH connections with private key authentication Nicklas Nordborg task major External files support 1.4 net.sf.basedb.xfiles
#1035 Upgrade SSHj library enhancement critical Open Grid Scheduler service v1.2 net.sf.basedb.opengrid
#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
#1055 Implement extension for logging in with OTP Nicklas Nordborg task major OTP login v1.0 net.sf.basedb.otp
#1039 Remove BouncyCastle jar files Nicklas Nordborg task critical Reggie v4.19 net.sf.basedb.reggie
#1056 Naming of child items Nicklas Nordborg defect blocker Reggie v4.19 net.sf.basedb.reggie
#1057 Description on *.dil items is incorrect Nicklas Nordborg defect major Reggie v4.19 net.sf.basedb.reggie
#1058 The "Download labels" button in the DNA/RNA/FlowThrough registration wizard doesn't work Nicklas Nordborg defect minor Reggie v4.19 net.sf.basedb.reggie
#1059 NullPointerException when running the Genotype quality control wizard and no patient has been registered for a specimen Nicklas Nordborg defect minor Reggie v4.19 net.sf.basedb.reggie
#1060 Copy consent in referral form registration wizard Nicklas Nordborg enhancement minor Reggie v4.19 net.sf.basedb.reggie
#1061 Display existing consent date in the consent form registration wizard Nicklas Nordborg enhancement trivial Reggie v4.19 net.sf.basedb.reggie
#1048 Release importer fails if the export contain integer enumerated annotation types defect critical Relax v1.3 net.sf.basedb.relax
#1062 OTP setup should not be allowed for multi-user accounts Nicklas Nordborg enhancement major OTP login v1.1 net.sf.basedb.otp
#1063 Specimen tube registration tries to register a new item with the same name as an existing item Nicklas Nordborg defect critical Reggie v4.19.1 net.sf.basedb.reggie
#1064 The temporary case used for holding consent information blocks registration of the real case Nicklas Nordborg defect critical Reggie v4.19.1 net.sf.basedb.reggie
#1065 It should be possible to search with PAD and RCCID number in case summary Nicklas Nordborg enhancement minor Reggie v4.19.1 net.sf.basedb.reggie
#1054 Even more functionality in the Flagged alignment wizard Nicklas Nordborg enhancement major Reggie v4.20 net.sf.basedb.reggie
#1066 Specimen tube registration wizard should allow different sampling and RNA later dates Nicklas Nordborg enhancement minor Reggie v4.20 net.sf.basedb.reggie
#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
#1069 Reggie should check actual active roles and not just membership Nicklas Nordborg defect minor 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
#1087 Changes needed for supporting multiple authentication managers Nicklas Nordborg enhancement critical OTP login v1.2 net.sf.basedb.otp
#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
#1086 Changes needed for supporting multiple authentication managers Nicklas Nordborg enhancement critical YubiKey v1.5 net.sf.basedb.yubikey
#1092 Detect configuration changes automatically Nicklas Nordborg enhancement major YubiKey v1.5 net.sf.basedb.yubikey
#1075 Change the release exporter to work with list of patients Nicklas Nordborg task major Reggie v4.21 net.sf.basedb.reggie
#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
#1079 The FrozenTissue date importer should ignore lines without date Nicklas Nordborg enhancement minor 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
#1082 HaplotypeCaller should not write command line parameters in result file Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1083 Add mBAF plot column to derived bioassay list Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1085 Remove the temporary hack for handling FlowThrough names with .f suffix Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1088 Keep Session Alive problems Nicklas Nordborg defect minor Reggie v4.21 net.sf.basedb.reggie
#1089 The Delivery client login should specify which login manager it uses Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1098 Release exporter should generate scripts that works with the "update" importer mode Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1100 The release exporter should set subtype on raw bioassay annotations Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1101 Annotation type categories for raw data types Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1103 Add permission check for downloading INCA report files Nicklas Nordborg defect critical Reggie v4.21 net.sf.basedb.reggie
#1104 Re-factor the INCA import Nicklas Nordborg enhancement major Reggie v4.21 net.sf.basedb.reggie
#1105 Lower-case 'c/d' suffix in the specimen tube registration wizard should be auto-converted to upper case Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1106 A pre-registered consent should prevent the "copy consent" function from appearing Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1107 Search by PATnnnn names in case summary Nicklas Nordborg enhancement minor Reggie v4.21 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
#1076 The Level 3 export plug-in should generate rsync script with -L option defect major Relax v1.4 net.sf.basedb.relax
#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
#1091 New annotation types in multiple new release version defect critical Relax v1.4 net.sf.basedb.relax
#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
#1097 Switch to BASE 3.13.1 task blocker Relax v1.4 net.sf.basedb.relax
#1099 The cohort exporter should have support for exporting downstream items Nicklas Nordborg task major Relax v1.4 net.sf.basedb.relax
#1102 The level3 exporter should use script templates enhancement minor Relax v1.4 net.sf.basedb.relax
#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
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