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

#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

#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

#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

#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

#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

#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

#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

#32 - Profile adding extra checks to "guessing" which record to decode

Issue - State: closed - Opened by davidadamsphd over 8 years ago - 1 comment