HadoopGenomics Hadoop-BAM issues

HadoopGenomics / 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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issues

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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