disq-bio/disq issues and pull requests

#182 - Bump io.netty:netty-codec-http from 4.0.56.Final to 4.1.108.Final

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#182 - Bump io.netty:netty-codec-http from 4.0.56.Final to 4.1.108.Final

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#181 - Bump org.apache.spark:spark-core_2.12 from 3.3.0 to 3.3.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#180 - Bump spark-core_2.12 from 3.3.0 to 3.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#179 - Bump htsjdk from 3.0.0 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#178 - Update dependency versions

Pull Request - State: closed - Opened by heuermh about 2 years ago - 3 comments

#177 - add tests on java 17

Pull Request - State: closed - Opened by lbergelson over 2 years ago - 5 comments

#176 - Update spark to 3.3.0

Pull Request - State: closed - Opened by lbergelson over 2 years ago - 1 comment

#175 - Update to htsjdk 3.0, change Allele->SimpleAllele.

Pull Request - State: closed - Opened by cmnbroad over 2 years ago

#174 - Rollback maven-failsafe-plugin version to 3.0.0-M4

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#173 - Use libcurl4-openssl-dev dependency to integration test workflow

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#172 - Add libcurl-dev install dependency to integration test workflow

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#171 - Add integration test Github Action workflow

Pull Request - State: closed - Opened by heuermh almost 3 years ago - 1 comment

#170 - Update google-cloud-nio dependency version to 0.123.20

Pull Request - State: open - Opened by heuermh almost 3 years ago

#169 - Update kryo-serializers dependency version to 0.45

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#168 - Update maven-failsafe-plugin version to 3.0.0-M5

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#167 - Update fmt-maven-plugin dependency version to 2.9.1

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#166 - NoClassDefFoundError: Could not initialize class org.eclipse.jetty.util.JavaVersion

Issue - State: closed - Opened by heuermh almost 3 years ago - 2 comments

#165 - Fix format errors reported by fmt-maven-plugin

Pull Request - State: closed - Opened by heuermh almost 3 years ago - 1 comment

#164 - Update samtools and bcftools to version 1.14

Pull Request - State: closed - Opened by cmnbroad almost 3 years ago - 3 comments

#163 - Reenable samtools read count cross checks in HtsjdkReadsRddTest.testReadIntervals

Issue - State: open - Opened by cmnbroad almost 3 years ago

#162 - Use sonatype-oss-release as release profile

Pull Request - State: closed - Opened by heuermh almost 3 years ago

#161 - Fix permissions for deploy snapshots Github Action

Issue - State: closed - Opened by heuermh almost 3 years ago - 1 comment

#160 - Migrate end-to-end tests from Travis CI to Github Actions

Issue - State: open - Opened by heuermh almost 3 years ago - 1 comment

#159 - Add CI and Deploy Snapshots workflows for Github Actions

Pull Request - State: closed - Opened by heuermh almost 3 years ago - 5 comments

#158 - HtsjdkReadsTraversalParameters serializable

Pull Request - State: closed - Opened by mwiewior almost 3 years ago

#157 - Update samtools and bcftools versions to 1.13

Pull Request - State: closed - Opened by heuermh over 3 years ago - 10 comments

#156 - Migrate CI off travis-ci.org

Issue - State: closed - Opened by heuermh over 3 years ago - 1 comment

#155 - Update samtools and bcftools versions to 1.13

Pull Request - State: closed - Opened by heuermh over 3 years ago - 2 comments

#154 - Update Spark dependency version to 3.1.2

Pull Request - State: closed - Opened by heuermh over 3 years ago - 2 comments

#153 - Update Spark dependency version to 3.1.2

Issue - State: closed - Opened by heuermh over 3 years ago

#152 - Update htsjdk dependency version to 2.24.1

Pull Request - State: closed - Opened by heuermh almost 4 years ago - 5 comments

#151 - Update Spark dependency version to 3.0.2

Pull Request - State: closed - Opened by heuermh almost 4 years ago - 1 comment

#150 - Updating maven-failsafe-plugin to 3.0.0-M5 fails CI integration tests under openjdk11

Issue - State: open - Opened by heuermh almost 4 years ago - 1 comment

#149 - Updating fmt-maven-plugin to 2.10 fails CI build

Issue - State: closed - Opened by heuermh almost 4 years ago

#148 - Update htsjdk dependency version to 2.23.0

Issue - State: closed - Opened by heuermh almost 4 years ago

#147 - [DISQ-148] Update htsjdk dependency version to 2.23.0

Pull Request - State: closed - Opened by heuermh almost 4 years ago - 3 comments

#146 - Updating kryo-serializers to 0.45 fails to build

Issue - State: closed - Opened by heuermh almost 4 years ago

#145 - Updating google-cloud-nio dependency to 0.122.5 fails unit tests

Issue - State: open - Opened by heuermh almost 4 years ago - 1 comment

#144 - 429 too many requests from github.com in Travis CI builds

Issue - State: closed - Opened by heuermh about 4 years ago

#143 - Bump junit from 4.12 to 4.13.1

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#142 - Update Spark dependency to version 3.0.1

Issue - State: closed - Opened by heuermh about 4 years ago

#141 - Updating to spark 3.0.1 and hadoop 3.2.1

Pull Request - State: closed - Opened by lbergelson over 4 years ago - 7 comments

#140 - Update Spark dependency version to 2.4.6

Pull Request - State: closed - Opened by heuermh over 4 years ago - 2 comments

#139 - Update Spark dependency version to 2.4.6

Issue - State: closed - Opened by heuermh over 4 years ago

#138 - Fix shard ordering bug on some filesystems.

Pull Request - State: open - Opened by lbergelson over 4 years ago - 4 comments

#137 - equal treatment for supplementary alignments

Pull Request - State: closed - Opened by tedsharpe over 4 years ago - 4 comments

#136 - Fixing RealWorldFilesIT (#132)

Pull Request - State: closed - Opened by lbergelson over 4 years ago - 3 comments

#135 - Fix failing tests in RealWorldFilesIT

Issue - State: closed - Opened by lbergelson over 4 years ago - 1 comment

#134 - Bump slf4j dependency version to 1.7.30

Pull Request - State: closed - Opened by heuermh over 4 years ago - 2 comments

#133 - Bump slf4j dependency to 1.7.30+

Issue - State: closed - Opened by heuermh over 4 years ago

#132 - Travis build failed in RealWorldFilesIT.testVariants

Issue - State: closed - Opened by heuermh almost 5 years ago - 6 comments

#131 - Update for htsjdk CRAM changes.

Pull Request - State: closed - Opened by cmnbroad almost 5 years ago - 3 comments

#130 - Add support for Spark 3

Issue - State: closed - Opened by heuermh almost 5 years ago - 5 comments

#129 - Update Maven plugin dependency versions

Pull Request - State: closed - Opened by heuermh almost 5 years ago - 3 comments

#128 - Bump Spark dependency version to 2.4.5

Pull Request - State: closed - Opened by heuermh almost 5 years ago - 1 comment

#127 - Bump htsjdk dependency version to 2.21.1

Pull Request - State: closed - Opened by heuermh almost 5 years ago - 1 comment

#126 - Split guessing fails with long reads

Issue - State: open - Opened by lbergelson almost 5 years ago
Labels: bug

#125 - Tiny cleanup of unecessary variable I noticed.

Pull Request - State: closed - Opened by lbergelson almost 5 years ago - 1 comment

#124 - Use results from SBI index instead of ignoring them

Pull Request - State: closed - Opened by lbergelson almost 5 years ago - 4 comments

#123 - BamSource doesn't return right when using SBIIndex

Issue - State: closed - Opened by wangdy12 almost 5 years ago - 1 comment

#122 - Bump Spark dependency version to 2.4.4.

Pull Request - State: closed - Opened by heuermh almost 5 years ago - 3 comments

#121 - Remove index merging code from src/htsjdk

Pull Request - State: closed - Opened by tomwhite about 5 years ago

#120 - add tests for SAM files that corrupt with adam + htsjdk 2.20.x

Pull Request - State: closed - Opened by heuermh about 5 years ago - 3 comments

#119 - Drop oraclejdk8 on travis since it is no longer supported

Pull Request - State: closed - Opened by tomwhite about 5 years ago - 1 comment

#118 - Warn on unrecognized options (fixes #25)

Pull Request - State: closed - Opened by tomwhite about 5 years ago - 3 comments

#117 - Fix calls to deprecated htsjdk APIs

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#116 - StackOverflowError when saving to BAM file in spark-shell

Issue - State: closed - Opened by heuermh over 5 years ago - 3 comments

#115 - Update release instructions following Louis' experience for 0.3.2

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#114 - Adding .idea directory to gitignore

Pull Request - State: closed - Opened by lbergelson over 5 years ago

#113 - Deploy snapshots in Travis build

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 6 comments

#112 - NotSerializableException: org.disq_bio.disq.HtsjdkReadsRdd in spark-shell

Issue - State: closed - Opened by heuermh over 5 years ago - 3 comments

#111 - Don't merge empty part files

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#110 - Downstream tools [GATK] affected by disq

Issue - State: closed - Opened by SHuang-Broad over 5 years ago - 6 comments

#109 - BAI merge for hg38 fails with OOM

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#108 - Cannot merge tabix files with different sequence names

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 4 comments
Labels: bug

#107 - Changes required to work with latest htsjdk

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 8 comments

#106 - Test on Java 11

Pull Request - State: closed - Opened by tomwhite over 5 years ago

#105 - Deploy snapshots in Travis build

Issue - State: closed - Opened by heuermh over 5 years ago - 4 comments

#104 - Reduce warning to info on unsuported concat operation.

Pull Request - State: closed - Opened by lbergelson over 5 years ago - 2 comments

#103 - Test large files on Travis

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 1 comment

#102 - Fix bug stream closed bug when merging BAI files greater than buffer size

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#101 - Secondary alignments can have an empty sequence.

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 1 comment

#100 - Is SeekableByteChannelPrefetcher still necessary?

Issue - State: closed - Opened by heuermh over 5 years ago - 2 comments

#99 - Log concatenation operation

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#98 - Adding git workflow, code style, voting sections to contributing doc.

Pull Request - State: closed - Opened by heuermh over 5 years ago

#97 - Write CRAI files when writing CRAM

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 2 comments

#96 - Run read tests on HDFS minicluster

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 3 comments

#94 - Parameterize Scala version

Pull Request - State: closed - Opened by tomwhite over 5 years ago - 11 comments

#93 - Read in parallel from NCBI Sequence Read Archive (SRA) format

Issue - State: open - Opened by heuermh over 5 years ago - 1 comment

#88 - Tests fail on Spark 2.4.0_2.12

Pull Request - State: closed - Opened by tomwhite almost 6 years ago - 4 comments

#84 - HTSJDK preview: CRAIEntry fields now need accessors

Pull Request - State: closed - Opened by jmthibault79 almost 6 years ago - 2 comments

#81 - Remove index merging code from src/htsjdk

Issue - State: closed - Opened by tomwhite almost 6 years ago - 3 comments

#66 - Cross-build across multiple Scala and Spark versions

Issue - State: closed - Opened by heuermh about 6 years ago - 9 comments

#59 - Shade HTSJDK classes into an alternate package

Issue - State: closed - Opened by heuermh about 6 years ago - 2 comments

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