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SequenceUtil.calculateMdAndNmTags does not match other methods
cram
#329
opened Sep 23, 2015 by
mattsooknah
CRAMIterator.next can throw NoSuchElementException when there are more records
bug
cram
#367
opened Nov 4, 2015 by
cmnbroad
Figure out there is a bug in BAMIndexMetaData.recordMetaData
cram
discussion
#401
opened Dec 2, 2015 by
lbergelson
CRAMFileReader query calls throw NPE on non-seekable input streams
cram
#426
opened Jan 6, 2016 by
cmnbroad
SAMFileWriterFactory doesn't use getDefaultCRAMReferenceSource
bug
cram
#472
opened Feb 12, 2016 by
cmnbroad
Ensure bam->cram->bam roundtripping is completely lossless
cram
#483
opened Feb 18, 2016 by
cmnbroad
SAM->CRAM->SAM round-tripping doesn't preserve unsigned attributes as unsigned
cram
#499
opened Feb 23, 2016 by
cmnbroad
SAMFileHeader in CRAM files is missing attributes required by the CRAM spec
cram
#506
opened Feb 29, 2016 by
cmnbroad
BAMIndexMetaData incorrect when index results from .crai->.bai conversion
cram
#531
opened Mar 21, 2016 by
cmnbroad
CRAMFileReader doesn't always honor index caching and memory mapping
cram
#535
opened Mar 22, 2016 by
cmnbroad
CRAMFileReader SAMRecordIterator implementations don't implement/honor assertSorted
cram
#547
opened Apr 1, 2016 by
cmnbroad
CRAM reader allows simultaneous iterators, but with inconsistent state
cram
#563
opened Apr 9, 2016 by
cmnbroad
Failure reading CRAM through SamReaderFactory from an FTP input stream
cram
#623
opened May 31, 2016 by
cmnbroad
Bam->CRAM doesn't always preserve cigar elements identically
cram
#713
opened Sep 22, 2016 by
cmnbroad
BAM->CRAM conversion doesn't handle supplementary reads correctly
cram
#802
opened Feb 10, 2017 by
cmnbroad
Error executing two sequential SamReader.queryOverlapping() calls for a CRAM File
bug
cram
#918
opened Jun 26, 2017 by
skashin
Reading a CRAM using a reference file with no dictionary gives misleading error message
bug
cram
#998
opened Sep 26, 2017 by
cmnbroad
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