JetBrains-Research big issues

JetBrains-Research / big

BigWIG, BigBED and TDF for the JVM

MIT License

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issues

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Remove logging implementation

#51 dievsky closed 3 years ago
1
Why do we need com.indeed.util-mmap

#50 dievsky closed 3 years ago
6
Migrate to Maven Central

#49 dievsky closed 3 years ago
1
reduce memory usage when computing summary

#48 yevshin opened 3 years ago
1
fix leaf bounds computation

#47 yevshin opened 3 years ago
1
Mention the library at https://research.jetbrains.org/groups/biolabs

#46 iromeo closed 3 years ago
3
Consistent `BedEntry.unpack`

#45 dievsky closed 5 years ago
1
BED parsing is sometimes too relaxed

#44 dievsky closed 5 years ago
0
Replace BED score type with Int

#43 dievsky closed 5 years ago
8
Adds a get-field-by-index method for ExtendedBedEntry

#42 dievsky closed 5 years ago
1
BedFormat data class

#41 dievsky opened 5 years ago
0
How to change chromosome names in a bigwig file?

#40 holgerbrandl closed 5 years ago
10
java.util.zip.DataFormatException: invalid distance too far back

#39 iromeo opened 6 years ago
0
Tdf file reading: Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836

#38 iromeo opened 6 years ago
0
Investigate possibility to configure multi platform builds on TeamCity

#37 olegs closed 6 years ago
1
Windows support

#36 iromeo closed 6 years ago
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 iromeo opened 6 years ago
0
java.lang.IllegalArgumentException: n must be >0

#34 iromeo closed 6 years ago
1
Encode *.bigBed files: NumberFormatException: For input string: "5.30862042004096"

#33 iromeo closed 6 years ago
3
Logging is too aggressive: AutoSQL queries are unsupported

#32 olegs closed 6 years ago
1
#1053

#31 PetrTsurinov closed 7 years ago
0
IllegalStateException: impossible "browser" section type in *.wig file

#30 iromeo closed 7 years ago
4
java.lang.IllegalArgumentException in BedEntry.<init>

#29 iromeo closed 7 years ago
2
Overflow on files larger than 2G

#28 superbobry closed 7 years ago
0
Support remote files

#27 superbobry closed 3 years ago
1
Streaming in 'BigFile#write'

#26 superbobry closed 8 years ago
0
Big files too big

#25 superbobry closed 8 years ago
0
Kotlin access error

#24 olegs closed 8 years ago
1
Get rid of 'ByteArrayInputStream'

#23 superbobry closed 8 years ago
1
Remove explicit synchronization in 'TdfFile'

#22 superbobry closed 8 years ago
1
Single ScoredInterval in wig and tdf

#21 olegs closed 8 years ago
3
Plugin dokka

#20 superbobry closed 8 years ago
0
Consider supporting CWig

#19 superbobry closed 8 years ago
1
Consider supporting smallWig

#18 superbobry closed 8 years ago
1
Add Logging for troubleshooting

#17 olegs closed 9 years ago
1
Interval slice artifacts

#16 iromeo closed 9 years ago
3
IllegalArgumentException: start must be <end

#15 iromeo closed 9 years ago
0
BigWig IOOBE

#14 iromeo closed 9 years ago
0
Pre-computed zoom levels

#13 superbobry closed 9 years ago
1
Cannot read big wig file saved using BigWig.write(..)

#12 iromeo closed 9 years ago
2
UCSC chromInfo.txt parsing error

#11 iromeo closed 9 years ago
1
Support reading gzipped chromosome sizes

#10 superbobry closed 9 years ago
0
Exception when reading ENCODE data

#9 superbobry closed 9 years ago
0
Encapsulate querying logic in 'BigFile'

#8 superbobry closed 9 years ago
0
Support AutoSQL

#7 superbobry opened 9 years ago
2
Implement BigWIG parsing

#6 superbobry closed 9 years ago
1
Test coverage for 'BigBedToBed'

#5 superbobry closed 9 years ago
1
Investigate how BigBED uses zoom levels and summary statistics

#4 superbobry closed 9 years ago
1
Implement 'BPlusTree#write'

#3 superbobry closed 9 years ago
0
Implement 'SeekableDataOutput'

#2 superbobry closed 9 years ago
1