JetBrains-Research/big

Issues

• Why do we need com.indeed.util-mmap

  #50 opened 4 years ago by dievsky
  6

• Remove logging implementation

  #51 opened 4 years ago by dievsky
  1

• Mention the library at https://research.jetbrains.org/groups/biolabs

  #46 opened 4 years ago by iromeo
  3

• Support remote files

  #27 opened 4 years ago by superbobry
  1

• Migrate to Maven Central

  #49 opened 4 years ago by dievsky
  1

• BED parsing is sometimes too relaxed

  #44 opened 5 years ago by dievsky
  0

• BedFormat data class

  #41 opened 6 years ago by dievsky
  0

• How to change chromosome names in a bigwig file?

  #40 opened 6 years ago by holgerbrandl
  10

• Investigate possibility to configure multi platform builds on TeamCity

  #37 opened 6 years ago by olegs
  1

• java.util.zip.DataFormatException: invalid distance too far back

  #39 opened 6 years ago by iromeo
  0

• Tdf file reading: Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836

  #38 opened 6 years ago by iromeo
  0

• Windows support

  #36 opened 7 years ago by iromeo
  2

• Tons of warnings like: [2018-03-13 00:51:40.839 WARN RTreeIndex] R+ tree leaves are overlapping: 23:[0; 48101538) ^ 23:[0; 44198477)

  #35 opened 7 years ago by iromeo
  0

• Logging is too aggressive: AutoSQL queries are unsupported

  #32 opened 7 years ago by olegs
  1

• Encode *.bigBed files: NumberFormatException: For input string: "5.30862042004096"

  #33 opened 7 years ago by iromeo
  3

• java.lang.IllegalArgumentException: n must be >0

  #34 opened 7 years ago by iromeo
  1

• Support AutoSQL

  #7 opened 10 years ago by superbobry
  2

• Overflow on files larger than 2G

  #28 opened 7 years ago by superbobry
  0

• java.lang.IllegalArgumentException in BedEntry.<init>

  #29 opened 7 years ago by iromeo
  2

• IllegalStateException: impossible "browser" section type in *.wig file

  #30 opened 7 years ago by iromeo
  4

• Streaming in 'BigFile#write'

  #26 opened 9 years ago by superbobry
  0

• Big files too big

  #25 opened 9 years ago by superbobry
  0

• Kotlin access error

  #24 opened 9 years ago by olegs
  1

• Consider supporting CWig

  #19 opened 9 years ago by superbobry
  1

• Consider supporting smallWig

  #18 opened 9 years ago by superbobry
  1

• Get rid of 'ByteArrayInputStream'

  #23 opened 9 years ago by superbobry
  1

• Remove explicit synchronization in 'TdfFile'

  #22 opened 9 years ago by superbobry
  1

• Plugin dokka

  #20 opened 9 years ago by superbobry
  0

• Single ScoredInterval in wig and tdf

  #21 opened 9 years ago by olegs
  3

• Add Logging for troubleshooting

  #17 opened 9 years ago by olegs
  1

• Pre-computed zoom levels

  #13 opened 9 years ago by superbobry
  1

• IllegalArgumentException: start must be <end

  #15 opened 9 years ago by iromeo
  0

• Interval slice artifacts

  #16 opened 9 years ago by iromeo
  3

• BigWig IOOBE

  #14 opened 9 years ago by iromeo
  0

• Cannot read big wig file saved using BigWig.write(..)

  #12 opened 9 years ago by iromeo
  2

• Implement 'SeekableDataOutput'

  #2 opened 10 years ago by superbobry
  1

• Implement 'BPlusTree#write'

  #3 opened 9 years ago by superbobry
  0

• Investigate how BigBED uses zoom levels and summary statistics

  #4 opened 9 years ago by superbobry
  1

• Implement BigWIG parsing

  #6 opened 9 years ago by superbobry
  1

• Encapsulate querying logic in 'BigFile'

  #8 opened 10 years ago by superbobry
  0

• Exception when reading ENCODE data

  #9 opened 9 years ago by superbobry
  0

• UCSC chromInfo.txt parsing error

  #11 opened 9 years ago by iromeo
  1

• Support reading gzipped chromosome sizes

  #10 opened 9 years ago by superbobry
  0

• Test coverage for 'BigBedToBed'

  #5 opened 9 years ago by superbobry
  1