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How to extract the UMI info in illumina read's name into a seperate tag
Priority: Medium
Status: Pending
In discussion to include in the project backlog
Type: Question
User/Developer question to be answer
#533
opened Nov 11, 2019 by
TendoLiu
GemMappabilityToBed has problems with some invalid characters in mappability files
Priority: Medium
Status: Pending
In discussion to include in the project backlog
Type: Question
User/Developer question to be answer
#531
opened Oct 19, 2018 by
robmaz
DownloadDistmapResult fails with many parts
Priority: Medium
Status: Pending
In discussion to include in the project backlog
Type: Question
User/Developer question to be answer
#530
opened Oct 18, 2018 by
robmaz
Better support for read groups in distmap integration
Priority: Medium
Status: Pending
In discussion to include in the project backlog
Type: Epic
Tasks that should be split in different issues
#518
opened Aug 24, 2018 by
magicDGS
Create a way to identify issues for beginners/newcomers
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Maintenance
Maintenance work (refactoring, build...)
#515
opened Aug 24, 2018 by
magicDGS
Support mixed dual/single indexed files in AssignReadGroupByBarcode
Priority: Medium
Status: Blocked
Blocked (in the project backlog)
Type: Enhancement
New features or improved behavior
#512
opened Aug 23, 2018 by
magicDGS
ReadsToDistmap: do not require maxReadLength
Priority: Medium
Status: Pending
In discussion to include in the project backlog
Type: Question
User/Developer question to be answer
#508
opened Aug 20, 2018 by
robmaz
Decide new theme or create one for help pages
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#507
opened Aug 14, 2018 by
magicDGS
Migrate docs to its own repository (or gh-pages branch)
Priority: High
Status: Accepted
Accepted in the project backlog
Type: Maintenance
Maintenance work (refactoring, build...)
#506
opened Aug 6, 2018 by
magicDGS
Move javadoc documentation to a service (or gh-pages branch)
Priority: High
Status: Blocked
Blocked (in the project backlog)
Type: Maintenance
Maintenance work (refactoring, build...)
#505
opened Aug 6, 2018 by
magicDGS
Start publishing ReadTools versions in maven central
Priority: High
Status: Blocked
Blocked (in the project backlog)
Type: Enhancement
New features or improved behavior
#504
opened Aug 6, 2018 by
magicDGS
Add support for indexing GemMappabilityToBed output
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#498
opened Jul 27, 2018 by
magicDGS
Add GemScoreMethod for "mappability sensu stricto"
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#494
opened Jul 27, 2018 by
magicDGS
Create factory for IO stream creation to be used reads but also other files
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#493
opened Jul 27, 2018 by
magicDGS
Support block-compressed FASTA reference
~gatk
Priority: Medium
Status: Blocked
Blocked (in the project backlog)
Type: Enhancement
New features or improved behavior
#489
opened Jul 26, 2018 by
magicDGS
Investigate performance of buffering for GemMappabilityReader
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#486
opened Jul 25, 2018 by
magicDGS
Force line-endings for UNIX on writers
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#484
opened Jul 15, 2018 by
magicDGS
Accept compressed gem-mappability inputs
Priority: High
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
#482
opened Jul 15, 2018 by
magicDGS
Add more unit tests to gem-mappability classes
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Test
Increase test coverage or add more test cases
#481
opened Jul 15, 2018 by
magicDGS
ComputeProperStatByWindow --stat does not show possible values in webpage
~barclay
Priority: Critical
Status: Blocked
Blocked (in the project backlog)
Type: Enhancement
New features or improved behavior
#469
opened Jun 5, 2018 by
magicDGS
Enhancements for ComputeProperStatByWindow
Priority: Medium
Status: Accepted
Accepted in the project backlog
Type: Epic
Tasks that should be split in different issues
#466
opened Jun 5, 2018 by
magicDGS
4 tasks
Decide defaults for RTReadWalker
Priority: Low
Status: Accepted
Accepted in the project backlog
Type: Question
User/Developer question to be answer
#465
opened Jun 5, 2018 by
magicDGS
Test RTHelpConstants static logging methods
Status: Accepted
Accepted in the project backlog
Type: Enhancement
New features or improved behavior
Type: Test
Increase test coverage or add more test cases
#460
opened Jun 1, 2018 by
magicDGS
Improve output format for ProperStatWindowEngine
Priority: Medium
Status: Blocked
Blocked (in the project backlog)
Type: Enhancement
New features or improved behavior
#459
opened Jun 1, 2018 by
magicDGS
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