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Use sequence dictionaries from interval files, when present
Engine
#301
opened Mar 12, 2015 by
droazen
Add a check in FeatureDataSource that intervals are sorted/merged properly
Engine
#327
opened Mar 23, 2015 by
droazen
Unify read comparators in hellbender
Engine
PRIORITY_LOW
QuixoticDream
#620
opened Jul 8, 2015 by
droazen
Consider running Travis Spark tests against EMR Spark
Help Wanted (Community)
Spark
#885
opened Sep 9, 2015 by
laserson
RevertBaseQualityScoresIntegrationTest needs CRAM tests
Picard
tests
#1232
opened Dec 2, 2015 by
akiezun
Add tests for different dup scoring strategies to AbstractMarkDuplicatesCommandLineProgramTest
tests
#1245
opened Dec 3, 2015 by
akiezun
ReadSparkSource.getHeader silently manufactures a bogus SAMFileHeader for ADAM (and possibly other) files
#1280
opened Dec 8, 2015 by
cmnbroad
port "Allow VariantsToTable to determine each allele's type when -SMA is used "
#1428
opened Jan 12, 2016 by
akiezun
create gradle plugin that automatically configures sparkJar correctly
QuixoticDream
ReleaseEngineering
#1453
opened Jan 27, 2016 by
lbergelson
Investigate whether our default validation stringency for reads should be STRICT rather than SILENT
Engine
question
#1457
opened Jan 28, 2016 by
droazen
Update serializable objects to use lambda functions where appropriate after upgrading to Kryo 3.0+
#1510
opened Feb 19, 2016 by
cwhelan
spark tools should warn if a splitting index isn't being used
Documentation
Spark
#1563
opened Mar 8, 2016 by
lbergelson
VariantFiltration - add a way to filter by AlleleBalance computed on the fly
enhancement
#1726
opened Apr 18, 2016 by
akiezun
GenotypeAnnotations require GT, but some fields could be computed without that information
community-request
#1730
opened Apr 19, 2016 by
magicDGS
Move NativeUtils class to gatk-native-bindings once it's available via maven
#1848
opened May 20, 2016 by
droazen
Document read-specific semantics of Locatable methods in GATKRead
#1976
opened Jul 5, 2016 by
droazen
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