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29 Open 66 Closed
29 Open 66 Closed
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Issues list

FastaInputFormat splits file into too many partitions
#207 opened Jan 18, 2020 by PatrycjaKarbownik
Double reads in BAMInputFormat
#206 opened Oct 9, 2019 by serash
NullPointerException at htsjdk CramNormalizer.getByteOrDefault with HDFS reference
#201 opened Jun 23, 2018 by heuermh
Reading sharded SAM / CRAM fails on some filesystems
#199 opened Jun 6, 2018 by lbergelson
2
Port Spark-BAM features
#196 opened Mar 14, 2018 by tomwhite
@tomwhite
6
Avoid unbounded memory allocation in BAM split guessing
#178 opened Dec 19, 2017 by tomwhite 8.0.0
Fix split guesser problems in spark-bam benchmark data
#177 opened Dec 19, 2017 by tomwhite 8.0.0
OutputFormats should write out the correct extension for their file type
#175 opened Dec 15, 2017 by fnothaft
Publish javadoc on GitHub
#173 opened Nov 23, 2017 by tomwhite 8.0.0
Add basic unit tests for classes with zero test coverage
#171 opened Nov 23, 2017 by tomwhite 8.0.0
Use Hadoop FileSystem concat to efficiently merge sharded BAM
#170 opened Nov 23, 2017 by tomwhite 8.0.0
1
Optimize BAM split generation for cloud stores
#169 opened Nov 23, 2017 by tomwhite 8.0.0
3
Change non-public top-level classes to be nested classes
#168 opened Nov 23, 2017 by tomwhite 8.0.0
Remove JAR with deps as there are no longer any tools
#160 opened Sep 25, 2017 by tomwhite 8.0.0
Remove StoppableOutputStream class used by VCFRecordWriter
#150 opened Sep 5, 2017 by cmnbroad
VCFHeaderReader BCF encoded file exception thrown for unrelated VCF header errors
#132 opened Jun 15, 2017 by heuermh
2
Code question
#119 opened Oct 13, 2016 by ryan-williams
2
CRAM container offsets should be updated by SAMFileMerger
#118 opened Oct 11, 2016 by cmnbroad
Add SamReaderFactory for sharded BAM files
#110 opened Jul 4, 2016 by tomwhite
Provide a way to specify a custom Deflater
#109 opened Jul 1, 2016 by akiezun
Add support for query interval semantics
#92 opened May 5, 2016 by tomwhite
Change htsjdk to avoid SAM header workaround in SAMRecordReader
#78 opened Mar 14, 2016 by tomwhite
Investigate generating bai indexes for BAM when writing from MR
#75 opened Mar 10, 2016 by tomwhite
SAMRecord.setHeader calls should be replaced with setHeaderStrict
#73 opened Feb 29, 2016 by cmnbroad
AnySAMOutputFormat should delegate to the appropriate RecordWriter
#72 opened Feb 29, 2016 by cmnbroad
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