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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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Update HTSJDK and Picard versions
#384
magicDGS
closed
6 years ago
2
Remove hack for RTHelpDocWorkUnitHandler
#383
magicDGS
closed
6 years ago
3
See if we can update HTSJDK before GATK 4.0.0.0
#382
magicDGS
closed
6 years ago
1
Upgrade GATK to 4.beta.6-87-g13bb6e0 SNAPSHOT
#381
magicDGS
closed
6 years ago
1
Use GATK's BaseTest for our base testing class
#380
magicDGS
closed
6 years ago
0
Upgrade GATK to 4.beta.6-45-g424bd95 (SNAPSHOT)
#379
magicDGS
closed
6 years ago
1
Upgrade GATK to 4.beta.6
#378
magicDGS
closed
6 years ago
3
TrimReads automatic help generation is broken
#377
magicDGS
closed
6 years ago
0
ReadWriterFactory.setReferencePath should use the SAMFileWriterFactory
#376
magicDGS
closed
6 years ago
1
ReadReaderFactory.setReferenceSequence
#375
magicDGS
closed
6 years ago
0
Use ArgumentsBuilder.hashCode in actual output tests
#374
magicDGS
closed
6 years ago
1
Use hashCode for ArgumentsBuilder for getting an unique name
#373
magicDGS
closed
6 years ago
0
Update GATK to released version
#372
magicDGS
closed
6 years ago
3
ReadGroupArgumentCollection should use Picard's arguments
#371
magicDGS
opened
6 years ago
0
Update program groups with GATK and Picard
#370
magicDGS
closed
6 years ago
3
BarcodeDictionaryFactory should use picard version of TabbedTextFileWithHeaderParser
#369
magicDGS
closed
6 years ago
0
Support CRAM input with java.nio.Path reference
#368
magicDGS
closed
6 years ago
1
Pull out AddOrReplaceReadGroups arguments to RTStandardArguments
#367
magicDGS
closed
6 years ago
1
ReadGroupArgumentCollection should not use GATK AddOrReplaceReadGroups args
#366
magicDGS
closed
6 years ago
2
Update TrimReadsFilterPluginArgumentCollection documentation
#365
magicDGS
closed
6 years ago
1
Add an hacked GATK's StandardArgumentDefinitions
#364
magicDGS
closed
6 years ago
3
Auto-detect pair/single end mode for single input file
#363
magicDGS
opened
6 years ago
0
Remove VersionEye badge
#362
magicDGS
closed
6 years ago
1
Update jacoco version to 0.8.0
#361
magicDGS
closed
6 years ago
1
Throw user exception for corrupted input
#360
magicDGS
closed
6 years ago
2
Catch "Premature end of file" error to throw an user exception for corrupted files
#359
magicDGS
closed
6 years ago
1
Add new params to ReadsToDistmap (and maybe ReadsToFastq)
#358
magicDGS
opened
6 years ago
0
Add better startup message for ReadTools
#357
magicDGS
opened
6 years ago
2
Check if the change in GATK's ReadClipper has downstream effects
#356
magicDGS
closed
6 years ago
3
Use the solution from hts-specs for MapReduce PG tag
#355
magicDGS
opened
6 years ago
0
Move standard argument definitions to RTStandardArguments
#354
magicDGS
closed
6 years ago
2
Update CHANGELOG with last changes
#353
magicDGS
closed
6 years ago
1
Fix commented test code in ReadsToDistmapIntegrationTest
#352
magicDGS
closed
6 years ago
1
TrimReadsTrimmerPluginArgumentCollection should be package-protected
#351
magicDGS
opened
6 years ago
1
Figure out why barclay warnings pop-up with the trimming arguments
#350
magicDGS
closed
6 years ago
1
Use the javadoc value pragma for hardcoded values
#349
magicDGS
opened
6 years ago
1
Implement BAM->FASTQ hts-spec translation scheme
#348
magicDGS
opened
6 years ago
0
Add trimming support for ReadsToDistmap
#347
magicDGS
closed
6 years ago
2
Use old-style argument names from GATK
#346
magicDGS
closed
6 years ago
6
Implement distmap MapReduce class for trimming
#345
magicDGS
closed
6 years ago
1
Add citation to Mol Ecol Resour
#344
magicDGS
closed
6 years ago
1
Add trimming support to ReadsToDistmap
#343
magicDGS
closed
6 years ago
0
Add published citation
#342
magicDGS
closed
6 years ago
0
Move VersionEye check and badge for Snyk.io
#341
magicDGS
closed
6 years ago
5
Follow kebab-case convention for param names
#340
magicDGS
opened
6 years ago
1
Release 1.1.0
#339
magicDGS
closed
7 years ago
3
Update CHANGELOG
#338
magicDGS
closed
7 years ago
1
Add docgen to release script
#337
magicDGS
closed
7 years ago
1
Test command-line header for metrics
#336
magicDGS
opened
7 years ago
0
Update documentation for trimming transformers
#335
magicDGS
closed
7 years ago
1
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