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magicDGS
/
ReadTools
A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
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TrimReads for popoolation error
#534
r-mashoodh
opened
3 years ago
0
How to extract the UMI info in illumina read's name into a seperate tag
#533
TendoLiu
opened
5 years ago
1
spurious assignment of read groups by barcodes with '+' delimiter
#532
AnnaMariaL
closed
5 years ago
7
GemMappabilityToBed has problems with some invalid characters in mappability files
#531
robmaz
opened
6 years ago
1
DownloadDistmapResult fails with many parts
#530
robmaz
opened
6 years ago
1
Release 1.5.2
#529
magicDGS
closed
6 years ago
1
Update CHANGELOG
#528
magicDGS
closed
6 years ago
1
Remove unused imports
#527
magicDGS
closed
6 years ago
2
Use quoted split pattern for barcodes
#526
magicDGS
closed
6 years ago
1
Default barcode separators should be treated separately for split
#525
magicDGS
closed
6 years ago
2
Specify that the property for default barcode separator is a regexp
#524
magicDGS
closed
6 years ago
1
Release 1.5.1
#523
magicDGS
closed
6 years ago
1
Update CHANGELOG
#522
magicDGS
closed
6 years ago
1
Clean up code and fix typos
#521
magicDGS
closed
6 years ago
2
Barcode file with empty header throws user error
#520
magicDGS
closed
6 years ago
2
Allow Casava formatted read names with barcode separators
#519
magicDGS
closed
6 years ago
1
Better support for read groups in distmap integration
#518
magicDGS
opened
6 years ago
1
Add stacktrace always to unexpected errors
#517
magicDGS
closed
6 years ago
1
Fix SRA Handbook link
#516
magicDGS
closed
6 years ago
1
Create a way to identify issues for beginners/newcomers
#515
magicDGS
opened
6 years ago
0
Add stacktrace to unexpected errors
#514
magicDGS
closed
6 years ago
0
Better error message for malformed header in barcode file
#513
magicDGS
closed
6 years ago
0
Support mixed dual/single indexed files in AssignReadGroupByBarcode
#512
magicDGS
opened
6 years ago
9
DownloadDistmapResult: merge SAM header (feature request)
#511
robmaz
closed
6 years ago
3
ReadsToDistmap: dump sam header somewhere (feature request)
#510
robmaz
closed
6 years ago
4
AssignReadGroupByBarcode: problem with doubly-barcoded reads
#509
robmaz
closed
6 years ago
6
ReadsToDistmap: do not require maxReadLength
#508
robmaz
opened
6 years ago
2
Decide new theme or create one for help pages
#507
magicDGS
opened
6 years ago
0
Migrate docs to its own repository (or gh-pages branch)
#506
magicDGS
opened
6 years ago
0
Move javadoc documentation to a service (or gh-pages branch)
#505
magicDGS
opened
6 years ago
1
Start publishing ReadTools versions in maven central
#504
magicDGS
opened
6 years ago
3
Update CHANGELOG with latest commits
#503
magicDGS
closed
6 years ago
1
Improve help for cli calling removed tools
#502
magicDGS
closed
6 years ago
1
Upgrade gradle to 4.9 and improve build
#501
magicDGS
closed
6 years ago
1
Correct sequence position for char error in GemMappabilityReader
#500
magicDGS
closed
6 years ago
2
Experimental GemMappabilityToBed does not work with a real dataset
#499
magicDGS
closed
6 years ago
2
Add support for indexing GemMappabilityToBed output
#498
magicDGS
opened
6 years ago
0
Release 1.5.0
#497
magicDGS
closed
6 years ago
1
Update CHANGELOG before release
#496
magicDGS
closed
6 years ago
0
Create tmp directory in scripts/prepare_release.sh
#495
magicDGS
closed
6 years ago
0
Add GemScoreMethod for "mappability sensu stricto"
#494
magicDGS
opened
6 years ago
0
Create factory for IO stream creation to be used reads but also other files
#493
magicDGS
opened
6 years ago
0
Update CHANGELOG with latest changes
#492
magicDGS
closed
6 years ago
1
Implement experimental GemMappabilityToBed tool
#491
magicDGS
closed
6 years ago
1
Update site dependencies
#490
magicDGS
closed
6 years ago
1
Support block-compressed FASTA reference
#489
magicDGS
opened
6 years ago
0
Implement deprecated tool registry to better error message if requested
#488
magicDGS
closed
6 years ago
0
Upgrade GATK to 4.0.6.0 and htsjdk to 2.16.0
#487
magicDGS
closed
6 years ago
2
Investigate performance of buffering for GemMappabilityReader
#486
magicDGS
opened
6 years ago
0
Force locale for base test class
#485
magicDGS
closed
6 years ago
1
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