HadoopGenomics/Hadoop-BAM

Issues

• Reformat source code for consistent use of whitespace

  #147 opened 4 years ago by heuermh
  2

• Reformat source code for consistent code style

  #148 opened 4 years ago by heuermh
  1

• Clarify copyright statement in license

  #165 opened 4 years ago by heuermh
  2

• Discuss project governance, relationships upstream and down

  #180 opened 4 years ago by heuermh
  27

• FastaInputFormat splits file into too many partitions

  #207 opened 5 years ago by PatrycjaKarbownik
  0

• Double reads in BAMInputFormat

  #206 opened 5 years ago by serash
  0

• Travis CI build fails due to oraclejdk

  #205 opened 5 years ago by heuermh
  0

• NullPointerException at htsjdk CramNormalizer.getByteOrDefault with HDFS reference

  #201 opened 6 years ago by heuermh
  0

• Reading sharded SAM / CRAM fails on some filesystems

  #199 opened 6 years ago by lbergelson
  2

• Hello, I would like to collaborate on your project as a translator to Spanish which is my native language

  #191 opened 7 years ago by LuigiBaute
  0

• Release Hadoop-BAM 7.10.0

  #198 opened 7 years ago by tomwhite
  1

• Port Spark-BAM features

  #196 opened 7 years ago by tomwhite
  6

• Use Hadoop FileSystem concat to efficiently merge sharded BAM

  #170 opened 7 years ago by tomwhite
  1

• 7.9.2 point release?

  #192 opened 7 years ago by fnothaft
  13

• Update dependencies to latest versions

  #172 opened 7 years ago by tomwhite
  0

• VCFRecordReader leaks IO resources

  #188 opened 7 years ago by fnothaft
  0

• SeekableStreams in BAMInputFormat.java aren't closed

  #187 opened 7 years ago by akmorrow13
  4

• VCFInputFormat leaks IO resources when detecting BCF vs. VCF from the data

  #184 opened 7 years ago by fnothaft
  0

• Remove deprecated classes in next major release

  #158 opened 7 years ago by tomwhite
  0

• Make Hadoop a provided dependency

  #159 opened 7 years ago by tomwhite
  0

• Avoid unbounded memory allocation in BAM split guessing

  #178 opened 7 years ago by tomwhite
  0

• Fix split guesser problems in spark-bam benchmark data

  #177 opened 7 years ago by tomwhite
  0

• Optimize BAM split generation for cloud stores

  #169 opened 7 years ago by tomwhite
  3

• Allow bad VCF rows to be waived with validation stringency

  #156 opened 7 years ago by fnothaft
  0

• OutputFormats should write out the correct extension for their file type

  #175 opened 7 years ago by fnothaft
  0

• BAMReordReader: CIGAR M operator maps off end of reference

  #174 opened 7 years ago by seppinho
  2

• Publish javadoc on GitHub

  #173 opened 7 years ago by tomwhite
  0

• Add basic unit tests for classes with zero test coverage

  #171 opened 7 years ago by tomwhite
  0

• Change non-public top-level classes to be nested classes

  #168 opened 7 years ago by tomwhite
  0

• Hadoop-BAM mvn test

  #117 opened 7 years ago by linhbngo
  2

• Enforce minimum Maven version

  #161 opened 7 years ago by tomwhite
  0

• NIOFileUtil.deleteRecursive delete if exists

  #131 opened 7 years ago by david-wb
  1

• Handle hg38 contig names

  #135 opened 7 years ago by tomwhite
  0

• Remove JAR with deps as there are no longer any tools

  #160 opened 7 years ago by tomwhite
  0

• VCFHeaderReader BCF encoded file exception thrown for unrelated VCF header errors

  #132 opened 7 years ago by heuermh
  2

• BAMRecordReader doesn't close I/O resources for index file

  #151 opened 7 years ago by fnothaft
  0

• Remove StoppableOutputStream class used by VCFRecordWriter

  #150 opened 7 years ago by cmnbroad
  0

• Should codepaths that use java.nio catch ProviderNotFoundException?

  #125 opened 7 years ago by fnothaft
  5

• Use slf4j logging instead of System.err.println

  #145 opened 7 years ago by heuermh
  0

• Add a way to get unmapped reads from a BAM

  #133 opened 7 years ago by tomwhite
  0

• Enable VCF output format to write GVCF

  #134 opened 7 years ago by tomwhite
  6

• Allow empty splitting-bai files

  #138 opened 7 years ago by tomwhite
  1

• Coveralls integration broken

  #128 opened 8 years ago by ryan-williams
  0

• Code question

  #119 opened 8 years ago by ryan-williams
  2

• AnySAMInputFormat ignores BAM read flags

  #126 opened 8 years ago by seppinho
  1

• CRAM container offsets should be updated by SAMFileMerger

  #118 opened 8 years ago by cmnbroad
  0

• Release Hadoop-BAM 7.7.0

  #115 opened 8 years ago by tomwhite
  1

• Not recognizing .bai extensions for index files

  #112 opened 8 years ago by jamesemery
  3

• Add SamReaderFactory for sharded BAM files

  #110 opened 8 years ago by tomwhite
  0

• Provide a way to specify a custom Deflater

  #109 opened 8 years ago by akiezun
  0