Skip to content

Issues: HadoopGenomics/Hadoop-BAM

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

29 Open 66 Closed
29 Open 66 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

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
ProTip! Exclude everything labeled bug with -label:bug.