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HadoopGenomics
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Hadoop-BAM
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
MIT License
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Bump htsjdk from 2.20.3 to 3.0.1
#216
dependabot[bot]
opened
1 year ago
0
Bump htsjdk from 1.133 to 3.0.1 in /examples
#215
dependabot[bot]
opened
1 year ago
0
[SECURITY] Fix Temporary File Information Disclosure Vulnerability
#214
JLLeitschuh
opened
1 year ago
0
[SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
#213
JLLeitschuh
opened
2 years ago
0
[SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
#212
JLLeitschuh
closed
2 years ago
0
Bump hadoop-client from 2.2.0 to 2.7.0 in /examples
#211
dependabot[bot]
opened
2 years ago
0
Bump junit from 4.12 to 4.13.1
#209
dependabot[bot]
opened
3 years ago
1
Bump junit from 4.8.1 to 4.13.1 in /examples
#208
dependabot[bot]
opened
3 years ago
1
FastaInputFormat splits file into too many partitions
#207
PatrycjaKarbownik
opened
4 years ago
0
Double reads in BAMInputFormat
#206
serash
opened
4 years ago
0
Travis CI build fails due to oraclejdk
#205
heuermh
closed
4 years ago
0
Use openjdk in Travis CI build
#204
heuermh
closed
4 years ago
3
add tests for SAM files that corrupt with adam + htsjdk 2.20.x
#203
heuermh
opened
4 years ago
5
bump htsjdk dependency version to 2.20.3
#202
heuermh
closed
4 years ago
5
NullPointerException at htsjdk CramNormalizer.getByteOrDefault with HDFS reference
#201
heuermh
opened
6 years ago
0
Ensure splits are sorted by path name
#200
tomwhite
opened
6 years ago
4
Reading sharded SAM / CRAM fails on some filesystems
#199
lbergelson
opened
6 years ago
2
Release Hadoop-BAM 7.10.0
#198
tomwhite
closed
6 years ago
1
delete shards as they're merged instead of afterwards
#197
lbergelson
closed
6 years ago
2
Port Spark-BAM features
#196
tomwhite
opened
6 years ago
6
Don't add a terminator when merging SAM files.
#195
tomwhite
closed
6 years ago
1
Changes to make it possible to subclass VCF and BCF input formats and…
#194
tomwhite
closed
6 years ago
1
Close unclosed IO resources in BAMInputFormat and util classes.
#193
heuermh
closed
6 years ago
3
7.9.2 point release?
#192
fnothaft
closed
6 years ago
13
Hello, I would like to collaborate on your project as a translator to Spanish which is my native language
#191
LuigiBaute
closed
6 years ago
0
Close unclosed IO resources in VCFRecordReader initialization.
#190
fnothaft
closed
6 years ago
2
closed streams detected by FindBugs
#189
akmorrow13
closed
6 years ago
3
VCFRecordReader leaks IO resources
#188
fnothaft
closed
6 years ago
0
SeekableStreams in BAMInputFormat.java aren't closed
#187
akmorrow13
closed
6 years ago
4
Update dependencies to latest versions (fixes #172).
#186
tomwhite
closed
6 years ago
1
Automatically close input stream in VCFInputFormat after inferring format.
#185
fnothaft
closed
6 years ago
1
VCFInputFormat leaks IO resources when detecting BCF vs. VCF from the data
#184
fnothaft
closed
6 years ago
0
Make Hadoop a provided dependency (fixes #159)
#183
tomwhite
closed
6 years ago
1
Reformat in line with the Google Java Style Guide
#182
tomwhite
opened
6 years ago
8
Remove deprecated classes and methods (#158)
#181
tomwhite
closed
6 years ago
1
Discuss project governance, relationships upstream and down
#180
heuermh
closed
3 years ago
27
Update BGZF block decode logic and refactor BGZFSplitGuesser on BaseSplitGuesser
#179
fnothaft
opened
6 years ago
1
Avoid unbounded memory allocation in BAM split guessing
#178
tomwhite
opened
6 years ago
0
Fix split guesser problems in spark-bam benchmark data
#177
tomwhite
opened
6 years ago
0
Specifies correct extensions for various file formats
#176
fnothaft
opened
6 years ago
2
OutputFormats should write out the correct extension for their file type
#175
fnothaft
opened
6 years ago
0
BAMReordReader: CIGAR M operator maps off end of reference
#174
seppinho
closed
6 years ago
2
Publish javadoc on GitHub
#173
tomwhite
opened
6 years ago
0
Update dependencies to latest versions
#172
tomwhite
closed
6 years ago
0
Add basic unit tests for classes with zero test coverage
#171
tomwhite
opened
6 years ago
0
Use Hadoop FileSystem concat to efficiently merge sharded BAM
#170
tomwhite
opened
6 years ago
1
Optimize BAM split generation for cloud stores
#169
tomwhite
opened
6 years ago
3
Change non-public top-level classes to be nested classes
#168
tomwhite
opened
6 years ago
0
Add options to use the Intel inflater or deflater when reading or
#167
tomwhite
closed
6 years ago
3
Deprecate BAMRecordWriter constructors that don't take a TaskAttemptC…
#166
tomwhite
closed
6 years ago
1
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