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Issues list

Extended API for symbolic alleles 1 - Ready dev feature
#18 opened May 23, 2014 by d-cameron vcf 4.3
Clean up Iterators / Iterables cleanup dev
#177 opened Feb 23, 2015 by mattsooknah
2
Refactor Filters to be functional interface cleanup dev user
#178 opened Feb 23, 2015 by lbergelson
2
replace clone() with copy constructors or factory methods cleanup dev
#192 opened Mar 7, 2015 by akiezun
3
Queries using empty intervals always produce no results. discussion
#204 opened Mar 19, 2015 by lbergelson
4
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
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
Javadocs for htsjdk.variant.* packages need formatting documentation
#253 opened May 18, 2015 by james-d
VariantContextBuilder does not perform a deep copy bug priority
#255 opened May 19, 2015 by d-cameron
@yfarjoun
5
Unexpected behaviour when parsing lists in INFO field bug
#261 opened Jun 1, 2015 by holtgrewe
3
Genotype.getAnyAttribute incorrectly handles converting int[] to List<Integer>
#274 opened Jul 1, 2015 by dfsurdyk
4
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
SamReader.queryUnmapped() does not return all unmapped reads
#278 opened Jul 2, 2015 by droazen
@droazen
3
htsjdk intermittent indexed fasta read errror
#310 opened Aug 22, 2015 by covingto
SequenceUtil.calculateMdAndNmTags does not match other methods cram
#329 opened Sep 23, 2015 by mattsooknah
1
Test for gzip extension fails for URLs with parameters
#332 opened Sep 24, 2015 by jrobinso
2
decodeInts returns null for PL with dots
#340 opened Oct 1, 2015 by raduvanciu
9
unmap read should also store the original sequence index
#352 opened Oct 16, 2015 by yfarjoun
@mattsooknah
CRAMIterator.next can throw NoSuchElementException when there are more records bug cram
#367 opened Nov 4, 2015 by cmnbroad
process for evolving api discussion
#378 opened Nov 9, 2015 by lbergelson
9
Figure out there is a bug in BAMIndexMetaData.recordMetaData cram discussion
#401 opened Dec 2, 2015 by lbergelson
1
Remove SRA related code and replace with a plugin API
#414 opened Dec 22, 2015 by tfenne
@droazen
28
htsjdk should parse multiallelic AF/AC
#423 opened Jan 5, 2016 by droazen
1
make 100% sure that allele ordering is preserved in htsjdk
#424 opened Jan 5, 2016 by droazen
CRAMFileReader query calls throw NPE on non-seekable input streams cram
#426 opened Jan 6, 2016 by cmnbroad
@cmnbroad
ProTip! Updated in the last three days: updated:>2024-12-11.