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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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Force line-endings for UNIX on writers
#484
magicDGS
opened
6 years ago
0
Force locale to english on tests
#483
magicDGS
closed
6 years ago
1
Accept compressed gem-mappability inputs
#482
magicDGS
opened
6 years ago
0
Add more unit tests to gem-mappability classes
#481
magicDGS
opened
6 years ago
0
Implement GEM-mappability reader
#480
magicDGS
closed
6 years ago
1
Update GATK to 4.0.6.0 (requires ReadTools-version in bioinformagik repo)
#479
magicDGS
closed
6 years ago
1
Upgrade gradle to 4.8.1 and plugin versions
#478
magicDGS
closed
6 years ago
1
Extend BaseTest to simplify RTBaseTest
#477
magicDGS
closed
6 years ago
2
Remove unneeded usages of GATKRead defensive getters
#476
magicDGS
closed
6 years ago
2
Release 1.4.1
#475
magicDGS
closed
6 years ago
1
Add latest fixes to CHANGELOG
#474
magicDGS
closed
6 years ago
1
Support java.nio.Path with FASTQ input files
#473
magicDGS
closed
6 years ago
1
Non-file FASTQ inputs does fail as inputs
#472
magicDGS
closed
6 years ago
1
Add DownloadDistmapResult check for _SUCCESS on startup
#471
magicDGS
closed
6 years ago
3
Add DownloadDistmapResult check for _SUCCESS files before processing
#470
magicDGS
closed
6 years ago
1
ComputeProperStatByWindow --stat does not show possible values in webpage
#469
magicDGS
opened
6 years ago
1
Release 1.4.0
#468
magicDGS
closed
6 years ago
1
Update CHANGELOG before release
#467
magicDGS
closed
6 years ago
1
Enhancements for ComputeProperStatByWindow
#466
magicDGS
opened
6 years ago
0
Decide defaults for RTReadWalker
#465
magicDGS
opened
6 years ago
0
Add ComputeProperStatByWindow experimental tool
#464
magicDGS
closed
6 years ago
1
Fix argument descriptions for PairIntegerTagListCounter
#463
magicDGS
closed
6 years ago
1
Share documentation String for --forceOverwrite
#462
magicDGS
closed
6 years ago
1
Check usages of GATKRead defensive copy methods and substitute for performance improvement
#461
magicDGS
closed
6 years ago
0
Test RTHelpConstants static logging methods
#460
magicDGS
opened
6 years ago
0
Improve output format for ProperStatWindowEngine
#459
magicDGS
opened
6 years ago
0
Evaluate performance improvements for ProperStatWindowEngine
#458
magicDGS
opened
6 years ago
0
Modify templates to integrate beta/experimental features
#457
magicDGS
closed
6 years ago
2
Implement ProperStatWindowEngine
#456
magicDGS
closed
6 years ago
1
Add formatter methods to RTHelpConstants and use in ReadToolsProgram
#455
magicDGS
closed
6 years ago
2
Fix NPE in PairIntegerTagCounter for missing tag
#454
magicDGS
closed
6 years ago
1
Update CHANGELOG with dependency changes
#453
magicDGS
closed
6 years ago
1
Upgrade HTSJDK to 2.15.0
#452
magicDGS
closed
6 years ago
1
Possible performance improvements for ProperStatWindowCalculator
#451
magicDGS
opened
6 years ago
0
Add ProperStatWindowCalculator
#450
magicDGS
closed
6 years ago
1
Decide cli-management for integer-tag counter arguments
#449
magicDGS
opened
6 years ago
0
Integrate read-stats as a barclay-plugin
#448
magicDGS
opened
6 years ago
0
Increase the codecov threshold for patch
#447
magicDGS
opened
6 years ago
0
Implement StatFunction interface
#446
magicDGS
closed
6 years ago
1
Document missing short arguments in next release
#445
magicDGS
closed
6 years ago
0
Add beta/experimental handling for help templates
#444
magicDGS
closed
6 years ago
0
Remove jitpack dependency and GATK-patched version
#443
magicDGS
opened
6 years ago
0
Upgrade to GATK 4.0.2.1-ReadTools and HTSJDK 1.14.3
#442
magicDGS
closed
6 years ago
3
Add ReadTools' ReadWalker implementation
#441
magicDGS
closed
6 years ago
1
Add new help formatter class for share between different walker classes
#440
magicDGS
closed
6 years ago
1
Implement ProperStatWindow* (Calculator and Engine)
#439
magicDGS
closed
6 years ago
0
Implement StatFunction interfaces and some implementations
#438
magicDGS
closed
6 years ago
0
Implement Experimental/Beta tool for computing statistic per-window
#437
magicDGS
closed
6 years ago
0
Tool for extract concrete read names from any source
#436
magicDGS
opened
6 years ago
0
Release 1.3.0
#435
magicDGS
closed
6 years ago
1
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