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266 Open 331 Closed
266 Open 331 Closed
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Issues list

Test for gzip extension fails for URLs with parameters
#332 opened Sep 24, 2015 by jrobinso
2
SequenceUtil.calculateMdAndNmTags does not match other methods cram
#329 opened Sep 23, 2015 by mattsooknah
1
htsjdk intermittent indexed fasta read errror
#310 opened Aug 22, 2015 by covingto
SamReader.queryUnmapped() does not return all unmapped reads
#278 opened Jul 2, 2015 by droazen
@droazen
3
VCFHeader class should allow multiple "other metadata" lines with the same key to be added VCFHeader Refactor Issues fixed by the header/line refactoring branch
#277 opened Jul 2, 2015 by droazen
1
@cmnbroad
1
Genotype.getAnyAttribute incorrectly handles converting int[] to List<Integer>
#274 opened Jul 1, 2015 by dfsurdyk
4
Unexpected behaviour when parsing lists in INFO field bug
#261 opened Jun 1, 2015 by holtgrewe
3
VariantContextBuilder does not perform a deep copy bug priority
#255 opened May 19, 2015 by d-cameron
@yfarjoun
5
Javadocs for htsjdk.variant.* packages need formatting documentation
#253 opened May 18, 2015 by james-d
VCFHeader should not strip version lines bug VCFHeader Refactor Issues fixed by the header/line refactoring branch
#251 opened May 13, 2015 by droazen vcf 4.3
@cmnbroad
VCFHeader class design is unsafe bug VCFHeader Refactor Issues fixed by the header/line refactoring branch
#250 opened May 13, 2015 by droazen
@cmnbroad
2
Queries using empty intervals always produce no results. discussion
#204 opened Mar 19, 2015 by lbergelson
4
replace clone() with copy constructors or factory methods cleanup dev
#192 opened Mar 7, 2015 by akiezun
3
Refactor Filters to be functional interface cleanup dev user
#178 opened Feb 23, 2015 by lbergelson
2
Clean up Iterators / Iterables cleanup dev
#177 opened Feb 23, 2015 by mattsooknah
2
Extended API for symbolic alleles 1 - Ready dev feature
#18 opened May 23, 2014 by d-cameron vcf 4.3
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