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Enforcing CRAM spec compliance (must have nonzero External Content ID) causes test failures
cram
#1232
opened Nov 29, 2018 by
jmthibault79
parsing missing values in VCF info field doesn't work
bug
#1228
opened Nov 21, 2018 by
davidbenjamin
Allele should contain a
MASKED_ANY_BASE
constant corresponding to N
.
#1226
opened Nov 14, 2018 by
jonn-smith
CRAM: Interaction between APDelta and Multi-Reference Slices
cram
#1218
opened Nov 1, 2018 by
jmthibault79
Htsjdk mangles unicode when writing sam files (and possibly bam/cram)
bug
#1202
opened Oct 24, 2018 by
lbergelson
CramComplianceTest: four tests from htslib fail due to SAMRecord mismatch
cram
#1189
opened Oct 5, 2018 by
jmthibault79
Consider removing IOException from ReferenceSequenceFile.close()
#1179
opened Sep 12, 2018 by
lbergelson
Refactor FASTA indexing to share implementation in input/output
#1173
opened Aug 10, 2018 by
magicDGS
htsjdk.samtools.util.RuntimeIOException: Could not find BCL file for cycle 26
#1171
opened Aug 1, 2018 by
kemin711
INFO/FORMAT fields with number of A, R, or G are not interpretable without defined ordering of alleles
#1170
opened Jul 31, 2018 by
bpow
fix DuplicateSetComparator to match the upstream changes to Markduplicates
#1163
opened Jul 9, 2018 by
yfarjoun
Querying for multiple loci in a BAM over NIO is unacceptably slow.
#1161
opened Jul 5, 2018 by
yfarjoun
CRAM NPE when writing using an unindexed fasta reference
cram
#1152
opened Jun 19, 2018 by
lbergelson
false positive in ReferenceSequenceFileFactory.canCreateIndexedFastaReader
#1143
opened Jun 7, 2018 by
lbergelson
Does IndexedFastaSequenceFile need to reset its channel in every read operation?
#1131
opened May 28, 2018 by
magicDGS
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