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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
The SamHeader system is vulnerable to tag "injection" when writing to SAM
#1108
opened Apr 24, 2018 by
yfarjoun
Can someone explain getMinimumOffset() from LinearIndex.java
#1107
opened Apr 18, 2018 by
betteridiot
BasicFastqWriter.write() flushes every call and writes inconsistent newlines
#1105
opened Apr 16, 2018 by
d-cameron
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