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Appetite for a non-backwards compatible upgrade to core APIs?
discussion
#520
opened Mar 10, 2016 by
tfenne
Htsjdk defines queryname sorting differently than samtools which can cause failures
#766
opened Dec 2, 2016 by
lbergelson
Output filenames containing the string ".bcf" result in BCF output instead of VCF
#761
opened Nov 28, 2016 by
jrandall
input streams opened from Paths fail when the underlying file is a pipe
#1084
opened Feb 8, 2018 by
lbergelson
Bring htsjdk's BCF2Codec up-to-date against the latest spec, and add tests
#628
opened Jun 2, 2016 by
droazen
Can HTSJDK use a VCF index to quickly count total records in a VCF?
#1586
opened Dec 10, 2021 by
bbimber
Why are Genotype.getAttributeAsX methods deprecated?
discussion
#866
opened Apr 27, 2017 by
lbergelson
Proposal for changes to Allele VariantContext, and Genotype Context for upstream deletion compatibility
#806
opened Feb 14, 2017 by
yfarjoun
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