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Ticket Summary Owner Type Priority Milestone Component
#539 Set "Disable log" flag on some annotation types Nicklas Nordborg enhancement blocker Reggie v2.16 net.sf.basedb.reggie
#547 Start Demux and Merge Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#548 Register Demux and Merge as ended Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#560 Use annotations on Histology work list to indicate progress Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#571 Update Reggie to new scripting pattern (first step) Nicklas Nordborg enhancement critical Reggie v2.16 net.sf.basedb.reggie
#578 Move to BASE 3.3 Nicklas Nordborg enhancement blocker Reggie v2.16 net.sf.basedb.reggie
#579 Store serial number of sequencers as annotations on hardware items Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#593 Start masking and alignment Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#595 Confirm alignment Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#613 Auto-detect tab or comma in Caliper-files Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#614 Improve error handling when executing jobs on the cluster Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#618 Specimen tube item is registered with incorrect name Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#619 Switching between cases will not always work Nicklas Nordborg defect minor Reggie v2.16 net.sf.basedb.reggie
#620 Tell browsers not to cache AJAX response data Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#621 Second specimen tube is not linked if registered before pathology referral Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#622 Updating a blood sample for a case with follow-up blood samples fails Nicklas Nordborg defect minor Reggie v2.16 net.sf.basedb.reggie
#623 Improve performance of the "Missing consent" export wizard Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#624 Improve performance of the "Missing data" export wizard Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#625 Prevent registration of patients with identical data Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#626 NullPointerException when registering follow-up blood Nicklas Nordborg defect trivial Reggie v2.16 net.sf.basedb.reggie
#627 Improve error visualization in wizards Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#631 Add data check to the confirm sequencing ended wizard Nicklas Nordborg enhancement major Reggie v2.16 net.sf.basedb.reggie
#632 Increase max volume limit in pooling wizard to 20µl Nicklas Nordborg enhancement minor Reggie v2.16 net.sf.basedb.reggie
#633 Adapter peak fraction=0 is displayed as 'unknown' in the pooling wizard Nicklas Nordborg defect trivial Reggie v2.16 net.sf.basedb.reggie
#636 INCA export may fail if there are blood samples with missing date Nicklas Nordborg defect major Reggie v2.16 net.sf.basedb.reggie
#637 Add annotations for lot numbers in the DNA/RNA/FlowThrough registration Nicklas Nordborg task major Reggie v2.16 net.sf.basedb.reggie
#639 Case summary may throw ItemNotFoundException Nicklas Nordborg defect trivial Reggie v2.16 net.sf.basedb.reggie
#643 Pathology referral form registration doesn't validate RNA later time Nicklas Nordborg defect minor Reggie v2.16.1 net.sf.basedb.reggie
#644 Can't start align job Nicklas Nordborg defect blocker Reggie v2.16.1 net.sf.basedb.reggie
#645 More than one parent item was found when starting align job Nicklas Nordborg defect blocker Reggie v2.16.1 net.sf.basedb.reggie
#646 New options for specimen type in specimen tube registration Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#647 Select specimen type per tube in specimen tube registration Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#648 More help texts in the specimen tube registration wizard Nicklas Nordborg enhancement trivial Reggie v2.16.1 net.sf.basedb.reggie
#649 Better balance in progress when demuxing Nicklas Nordborg enhancement trivial Reggie v2.16.1 net.sf.basedb.reggie
#653 Use explicit paths to all important program used in pipeline Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#654 Synchronize default options for pipeline analysis Nicklas Nordborg enhancement minor Reggie v2.16.1 net.sf.basedb.reggie
#655 PT_READS is not reported correctly in description for FASTQ files Nicklas Nordborg defect major Reggie v2.16.1 net.sf.basedb.reggie
#656 FASTQ files are not always stored in the expected folder Nicklas Nordborg defect critical Reggie v2.16.1 net.sf.basedb.reggie
#657 Include Reggie version number in wizards Nicklas Nordborg enhancement minor Reggie v2.16.1 net.sf.basedb.reggie
#658 Adjust fragment size mean and standard deviation Nicklas Nordborg enhancement critical Reggie v2.16.1 net.sf.basedb.reggie
#659 Do not trust fragement size calculated by bowtie if number of used fragments is too low Nicklas Nordborg enhancement major Reggie v2.16.1 net.sf.basedb.reggie
#660 Error in sample source report wizard Nicklas Nordborg defect major Reggie v2.16.1 net.sf.basedb.reggie
#661 Calculate average fragment size and standard deviation after tophat Nicklas Nordborg enhancement major Reggie v2.16.2 net.sf.basedb.reggie
#662 Race conditions in demux script Nicklas Nordborg defect critical Reggie v2.16.2 net.sf.basedb.reggie
#663 Demux script should not gzip FASTQ files until the last step Nicklas Nordborg enhancement major Reggie v2.16.2 net.sf.basedb.reggie
#664 Display pool names in confirm demux wizard Nicklas Nordborg enhancement minor Reggie v2.16.2 net.sf.basedb.reggie
#665 Display pool name in warning messages Nicklas Nordborg enhancement minor Reggie v2.16.2 net.sf.basedb.reggie
#666 Default number of slots for demux should be 4 Nicklas Nordborg enhancement trivial Reggie v2.16.2 net.sf.basedb.reggie
#667 Library registration wizard complains about missing concentration for Stratagene Nicklas Nordborg defect critical Reggie v2.16.3 net.sf.basedb.reggie
#526 Retraction wizard olle task major Reggie v2.17 net.sf.basedb.reggie
#630 Start cufflinks Nicklas Nordborg task critical Reggie v2.17 net.sf.basedb.reggie
#638 Fix issues with not filling all pools on a a plate Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#640 Finalize update to new scripting pattern Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#641 Import data from cufflinks result files Nicklas Nordborg task critical Reggie v2.17 net.sf.basedb.reggie
#642 Confirm feature extraction as completed Nicklas Nordborg task major Reggie v2.17 net.sf.basedb.reggie
#650 New type of specimen core biopsy Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#651 Add 1x16 pool schema to create mRNA plate wizard Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#668 Cache result of queries used to count items on Reggie index page Nicklas Nordborg enhancement minor Reggie v2.17 net.sf.basedb.reggie
#669 RNAQC Caliper well table import wizard should check if values are missing Nicklas Nordborg defect critical Reggie v2.17 net.sf.basedb.reggie
#670 Echo commands used for tophat, etc to *.out files Nicklas Nordborg enhancement minor Reggie v2.17 net.sf.basedb.reggie
#671 Save reggie version with jobs Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#675 Running a mask/align job as debug for a non-debug demux doesn't change the outcome Nicklas Nordborg defect minor Reggie v2.17 net.sf.basedb.reggie
#677 ant 'clean' should delete downloaded BASE JAR files Nicklas Nordborg task minor Reggie v2.17 net.sf.basedb.reggie
#678 Operator delivery comment in specimen tube registration wizard is not saved Nicklas Nordborg defect major Reggie v2.17 net.sf.basedb.reggie
#681 Run CheckIlluminaDirectory from a cluster node instead of the cluster controller Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#682 Improve performance when submitting jobs to cluster Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#683 Do not start processes in the background Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#684 Run picard AddOrReplaceReadGroups after alignment Nicklas Nordborg enhancement major Reggie v2.17 net.sf.basedb.reggie
#685 New Bowtie version 2.2.4 Nicklas Nordborg enhancement minor Reggie v2.17 net.sf.basedb.reggie
#686 Limit jobs to 16 slots by default Nicklas Nordborg enhancement minor Reggie v2.17 net.sf.basedb.reggie
#687 ApWeight field in partition wizard doesn't auto-tab on ENTER key Nicklas Nordborg defect major Reggie v2.17.1 net.sf.basedb.reggie
#688 Depend on BASE 3.3.3 Nicklas Nordborg task major Reggie v2.17.1 net.sf.basedb.reggie
#694 Path-element tags should use subclass instad of clazz Nicklas Nordborg defect trivial Reggie v2.17.1 net.sf.basedb.reggie
#697 Can't start alignment if there are libraries without a library plate Nicklas Nordborg defect critical Reggie v2.17.2 net.sf.basedb.reggie
#698 Set number of nodes in the demux wizard Nicklas Nordborg enhancement minor Reggie v2.17.2 net.sf.basedb.reggie
#699 Library registration doesn't warn about missing values in Caliper well table CSV Nicklas Nordborg defect major Reggie v2.17.2 net.sf.basedb.reggie
#700 Missing '-' between plate name and library name in start alignment and start cufflinks wizards Nicklas Nordborg defect major Reggie v2.17.3 net.sf.basedb.reggie
#628 Add right-click menu to create pools wizard Nicklas Nordborg enhancement minor Reggie v2.18 net.sf.basedb.reggie
#635 Include analysis information in the case summary Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#672 RNA concentration normalization wizard Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#673 Register RNA QC results from BioAnalyzer runs Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#674 Generate document with report of sequencing results Nicklas Nordborg task critical Reggie v2.18 net.sf.basedb.reggie
#676 Switch to AGPL v3 license Nicklas Nordborg task blocker Reggie v2.18 net.sf.basedb.reggie
#679 Configuration file improvments Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#680 Cleanup script for PostgreSQL development clone Nicklas Nordborg task minor Reggie v2.18 net.sf.basedb.reggie
#689 Use new script for checking Illumina data files Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#691 Items in case summary are not sorted Nicklas Nordborg defect minor Reggie v2.18 net.sf.basedb.reggie
#692 Some icons in case summary are broken in print version Nicklas Nordborg defect minor Reggie v2.18 net.sf.basedb.reggie
#693 Move debug utilities to a toolbar at bottom of page Nicklas Nordborg enhancement minor Reggie v2.18 net.sf.basedb.reggie
#701 Check compability with BASE 3.4 Nicklas Nordborg enhancement major Reggie v2.18 net.sf.basedb.reggie
#704 NullPointerException in retraction servlet when entering a case name that doesn't exist Nicklas Nordborg defect major Reggie v2.18 net.sf.basedb.reggie
#705 Remove internal sorting methods in retraction servlet Nicklas Nordborg enhancement minor Reggie v2.18 net.sf.basedb.reggie
#690 MeLuDi - Registration wizard for melanoma-lung cancer projects olle task major MeLuDi v1.0 net.sf.basedb.meludi
#710 Flow cells can be counted multiple times for 'Register sequencing started' Nicklas Nordborg defect minor Reggie v2.18.1 net.sf.basedb.reggie
#711 The 'Confirm sequencing completed' wizard should not set FirstBaseReportFailed on flow cell Nicklas Nordborg enhancement minor Reggie v2.18.1 net.sf.basedb.reggie
#713 Comment for bioplate in RNA dilution registration is not updated Nicklas Nordborg defect major Reggie v2.18.1 net.sf.basedb.reggie
#719 NullPointerException in extraction registration wizard Nicklas Nordborg defect critical Reggie v2.18.1 net.sf.basedb.reggie
#718 MeLuDi v.1.0 bug fixes and improvements olle task major MeLuDi v1.1 net.sf.basedb.meludi
#727 RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells Nicklas Nordborg defect critical Reggie v2.18.2 net.sf.basedb.reggie
#712 The 'Skin options' menu is only visible for root user defect minor Skin-collection 1.1 net.sf.basedb.skincollection
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