Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / HadoopGenomics/Hadoop-BAM issues and pull requests
#216 - Bump htsjdk from 2.20.3 to 3.0.1
Pull Request -
State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies
#215 - Bump htsjdk from 1.133 to 3.0.1 in /examples
Pull Request -
State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies
#214 - [SECURITY] Fix Temporary File Information Disclosure Vulnerability
Pull Request -
State: open - Opened by JLLeitschuh over 1 year ago
#213 - [SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
Pull Request -
State: open - Opened by JLLeitschuh almost 2 years ago
#212 - [SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
Pull Request -
State: closed - Opened by JLLeitschuh almost 2 years ago
#211 - Bump hadoop-client from 2.2.0 to 2.7.0 in /examples
Pull Request -
State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies
#209 - Bump junit from 4.12 to 4.13.1
Pull Request -
State: open - Opened by dependabot[bot] over 3 years ago
- 1 comment
Labels: dependencies
#208 - Bump junit from 4.8.1 to 4.13.1 in /examples
Pull Request -
State: open - Opened by dependabot[bot] over 3 years ago
- 1 comment
Labels: dependencies
#207 - FastaInputFormat splits file into too many partitions
Issue -
State: open - Opened by PatrycjaKarbownik over 4 years ago
#206 - Double reads in BAMInputFormat
Issue -
State: open - Opened by serash over 4 years ago
#205 - Travis CI build fails due to oraclejdk
Issue -
State: closed - Opened by heuermh almost 5 years ago
#204 - Use openjdk in Travis CI build
Pull Request -
State: closed - Opened by heuermh almost 5 years ago
- 3 comments
#203 - add tests for SAM files that corrupt with adam + htsjdk 2.20.x
Pull Request -
State: open - Opened by heuermh almost 5 years ago
- 5 comments
#202 - bump htsjdk dependency version to 2.20.3
Pull Request -
State: closed - Opened by heuermh almost 5 years ago
- 5 comments
#201 - NullPointerException at htsjdk CramNormalizer.getByteOrDefault with HDFS reference
Issue -
State: open - Opened by heuermh about 6 years ago
#200 - Ensure splits are sorted by path name
Pull Request -
State: open - Opened by tomwhite about 6 years ago
- 4 comments
#199 - Reading sharded SAM / CRAM fails on some filesystems
Issue -
State: open - Opened by lbergelson about 6 years ago
- 2 comments
#198 - Release Hadoop-BAM 7.10.0
Issue -
State: closed - Opened by tomwhite about 6 years ago
- 1 comment
#197 - delete shards as they're merged instead of afterwards
Pull Request -
State: closed - Opened by lbergelson over 6 years ago
- 2 comments
#196 - Port Spark-BAM features
Issue -
State: open - Opened by tomwhite over 6 years ago
- 6 comments
#195 - Don't add a terminator when merging SAM files.
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#194 - Changes to make it possible to subclass VCF and BCF input formats and…
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#193 - Close unclosed IO resources in BAMInputFormat and util classes.
Pull Request -
State: closed - Opened by heuermh over 6 years ago
- 3 comments
#192 - 7.9.2 point release?
Issue -
State: closed - Opened by fnothaft over 6 years ago
- 13 comments
#191 - Hello, I would like to collaborate on your project as a translator to Spanish which is my native language
Issue -
State: closed - Opened by LuigiBaute over 6 years ago
#190 - Close unclosed IO resources in VCFRecordReader initialization.
Pull Request -
State: closed - Opened by fnothaft over 6 years ago
- 2 comments
#189 - closed streams detected by FindBugs
Pull Request -
State: closed - Opened by akmorrow13 over 6 years ago
- 3 comments
#188 - VCFRecordReader leaks IO resources
Issue -
State: closed - Opened by fnothaft over 6 years ago
#187 - SeekableStreams in BAMInputFormat.java aren't closed
Issue -
State: closed - Opened by akmorrow13 over 6 years ago
- 4 comments
#186 - Update dependencies to latest versions (fixes #172).
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#185 - Automatically close input stream in VCFInputFormat after inferring format.
Pull Request -
State: closed - Opened by fnothaft over 6 years ago
- 1 comment
#184 - VCFInputFormat leaks IO resources when detecting BCF vs. VCF from the data
Issue -
State: closed - Opened by fnothaft over 6 years ago
#183 - Make Hadoop a provided dependency (fixes #159)
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#182 - Reformat in line with the Google Java Style Guide
Pull Request -
State: open - Opened by tomwhite over 6 years ago
- 8 comments
#181 - Remove deprecated classes and methods (#158)
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#180 - Discuss project governance, relationships upstream and down
Issue -
State: closed - Opened by heuermh over 6 years ago
- 27 comments
#179 - Update BGZF block decode logic and refactor BGZFSplitGuesser on BaseSplitGuesser
Pull Request -
State: open - Opened by fnothaft over 6 years ago
- 1 comment
#178 - Avoid unbounded memory allocation in BAM split guessing
Issue -
State: open - Opened by tomwhite over 6 years ago
#177 - Fix split guesser problems in spark-bam benchmark data
Issue -
State: open - Opened by tomwhite over 6 years ago
#176 - Specifies correct extensions for various file formats
Pull Request -
State: open - Opened by fnothaft over 6 years ago
- 2 comments
#175 - OutputFormats should write out the correct extension for their file type
Issue -
State: open - Opened by fnothaft over 6 years ago
#174 - BAMReordReader: CIGAR M operator maps off end of reference
Issue -
State: closed - Opened by seppinho over 6 years ago
- 2 comments
#173 - Publish javadoc on GitHub
Issue -
State: open - Opened by tomwhite over 6 years ago
#172 - Update dependencies to latest versions
Issue -
State: closed - Opened by tomwhite over 6 years ago
#171 - Add basic unit tests for classes with zero test coverage
Issue -
State: open - Opened by tomwhite over 6 years ago
#170 - Use Hadoop FileSystem concat to efficiently merge sharded BAM
Issue -
State: open - Opened by tomwhite over 6 years ago
- 1 comment
#169 - Optimize BAM split generation for cloud stores
Issue -
State: open - Opened by tomwhite over 6 years ago
- 3 comments
#168 - Change non-public top-level classes to be nested classes
Issue -
State: open - Opened by tomwhite over 6 years ago
#167 - Add options to use the Intel inflater or deflater when reading or
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 3 comments
#166 - Deprecate BAMRecordWriter constructors that don't take a TaskAttemptC…
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 1 comment
#165 - Clarify copyright statement in license
Issue -
State: closed - Opened by heuermh over 6 years ago
- 2 comments
#164 - Decode BAM fields eagerly in BAMSplitGuesser when verifying 3 records…
Pull Request -
State: closed - Opened by tomwhite over 6 years ago
- 10 comments
#163 - In NIOFileUtil.deleteRecursive only delete directory if it exists.
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 2 comments
#162 - Require at least mvn 3.3.9 and java 1.8
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 1 comment
#161 - Enforce minimum Maven version
Issue -
State: closed - Opened by tomwhite almost 7 years ago
#160 - Remove JAR with deps as there are no longer any tools
Issue -
State: open - Opened by tomwhite almost 7 years ago
#159 - Make Hadoop a provided dependency
Issue -
State: closed - Opened by tomwhite almost 7 years ago
#158 - Remove deprecated classes in next major release
Issue -
State: closed - Opened by tomwhite almost 7 years ago
#157 - Support specifying validation stringency in VCFRecordReader.
Pull Request -
State: closed - Opened by fnothaft almost 7 years ago
- 11 comments
#156 - Allow bad VCF rows to be waived with validation stringency
Issue -
State: closed - Opened by fnothaft almost 7 years ago
#155 - Extracts Interval parsing common code from BAMFileFormat and VCFFileFo…
Pull Request -
State: closed - Opened by vruano almost 7 years ago
- 6 comments
#154 - Reformat source code for consistent code style
Pull Request -
State: closed - Opened by heuermh almost 7 years ago
- 4 comments
#153 - Reformat source code for consistent use of whitespace.
Pull Request -
State: closed - Opened by heuermh almost 7 years ago
- 11 comments
#152 - Close all BAM-related I/O resources in BAMRecordReader.
Pull Request -
State: closed - Opened by fnothaft almost 7 years ago
- 1 comment
#151 - BAMRecordReader doesn't close I/O resources for index file
Issue -
State: closed - Opened by fnothaft almost 7 years ago
#150 - Remove StoppableOutputStream class used by VCFRecordWriter
Issue -
State: open - Opened by cmnbroad almost 7 years ago
#149 - Fixes issue in BGZFSplitGuesser relating to incomplete copy.
Pull Request -
State: closed - Opened by fnothaft almost 7 years ago
- 1 comment
#148 - Reformat source code for consistent code style
Issue -
State: closed - Opened by heuermh almost 7 years ago
- 1 comment
#147 - Reformat source code for consistent use of whitespace
Issue -
State: closed - Opened by heuermh almost 7 years ago
- 2 comments
#146 - Use slf4j logging instead of System.err.println
Pull Request -
State: closed - Opened by heuermh almost 7 years ago
- 4 comments
#145 - Use slf4j logging instead of System.err.println
Issue -
State: closed - Opened by heuermh almost 7 years ago
#144 - Use new, more efficient, OverlapsDetector API
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 1 comment
#143 - Improve creation of child path in VCFFileMerger for GCS
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 1 comment
#142 - Eliminate buffer copy bug in BGZFSplitGuesser.
Pull Request -
State: closed - Opened by fnothaft almost 7 years ago
- 5 comments
#141 - Upgrade to htsjdk 2.11.0.
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 3 comments
#140 - Add codepath to calculate splits from BAM index.
Pull Request -
State: closed - Opened by fnothaft almost 7 years ago
- 21 comments
#139 - Filter out splitting bai from splits and allow empty splitting-bai files
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 1 comment
#138 - Allow empty splitting-bai files
Issue -
State: closed - Opened by tomwhite almost 7 years ago
- 1 comment
#137 - Allow custom VariantContextWriter to be specified in VCFRecordWriter …
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 2 comments
#136 - Add a way to get unmapped reads from a BAM.
Pull Request -
State: closed - Opened by tomwhite almost 7 years ago
- 5 comments
#135 - Handle hg38 contig names
Issue -
State: closed - Opened by tomwhite almost 7 years ago
#134 - Enable VCF output format to write GVCF
Issue -
State: closed - Opened by tomwhite almost 7 years ago
- 6 comments
#133 - Add a way to get unmapped reads from a BAM
Issue -
State: closed - Opened by tomwhite almost 7 years ago
#132 - VCFHeaderReader BCF encoded file exception thrown for unrelated VCF header errors
Issue -
State: open - Opened by heuermh about 7 years ago
- 2 comments
#131 - NIOFileUtil.deleteRecursive delete if exists
Issue -
State: closed - Opened by david-wb about 7 years ago
- 1 comment
#130 - Catch ProviderNotFoundException when picking BAM splits, and formally…
Pull Request -
State: closed - Opened by fnothaft about 7 years ago
- 4 comments
#129 - fix coveralls reporting
Pull Request -
State: closed - Opened by ryan-williams about 7 years ago
- 2 comments
#128 - Coveralls integration broken
Issue -
State: closed - Opened by ryan-williams about 7 years ago
#127 - use log4j instead of System.err.printlns
Pull Request -
State: closed - Opened by ryan-williams about 7 years ago
- 3 comments
#126 - AnySAMInputFormat ignores BAM read flags
Issue -
State: closed - Opened by seppinho about 7 years ago
- 1 comment
#125 - Should codepaths that use java.nio catch ProviderNotFoundException?
Issue -
State: closed - Opened by fnothaft about 7 years ago
- 5 comments
#124 - fix FastaInputFormat infinite loop
Pull Request -
State: closed - Opened by ryan-williams over 7 years ago
- 1 comment
#122 - Use htsjdk machinery to make reading with intervals significantly faster
Pull Request -
State: closed - Opened by tomwhite over 7 years ago
- 5 comments
#121 - Improve performance for large interval lists
Pull Request -
State: closed - Opened by tomwhite over 7 years ago
- 5 comments
#119 - Code question
Issue -
State: open - Opened by ryan-williams over 7 years ago
- 2 comments
#117 - Hadoop-BAM mvn test
Issue -
State: closed - Opened by linhbngo almost 8 years ago
- 2 comments
#105 - Use new OverlapsDetector API
Issue -
State: closed - Opened by tomwhite about 8 years ago
#69 - squid:S1118 - Utility classes should not have public constructors
Pull Request -
State: closed - Opened by m-ezzat over 8 years ago
- 1 comment
#33 - Add extra check to finding split point via guessing (if profiling says it's fine)
Issue -
State: closed - Opened by davidadamsphd over 8 years ago
- 1 comment
#32 - Profile adding extra checks to "guessing" which record to decode
Issue -
State: closed - Opened by davidadamsphd over 8 years ago
- 1 comment