hammerlab/guacamole issues and pull requests

#617 - upgrade hammerlab/spark-genomics deps

Pull Request - State: open - Opened by ryan-williams almost 8 years ago - 2 comments

#616 - Get guacamole and friends building on newest batch of shared libraries

Issue - State: open - Opened by hammer about 8 years ago - 1 comment
Labels: infrastructure

#615 - Make indel realignment splice aware

Issue - State: open - Opened by hammer about 8 years ago - 1 comment

#614 - port to SBT, factor out more components, upgrade some deps

Pull Request - State: closed - Opened by ryan-williams about 8 years ago - 3 comments

#613 - Factor out some reusable components to other repos

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#612 - Upgrades and default settings to SomaticStandard

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

#611 - --loci argument conflicts with TakeLociIterator

Issue - State: open - Opened by arahuja over 8 years ago - 2 comments

#610 - add --split-size arg

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 6 comments

#609 - rm some test boilerplate

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#608 - Add loci set intersection and difference methods

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

#607 - clean up test-kryo-registrations

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#606 - loci-parsing refactor

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#605 - Remove PileupFilter and revamp InputFilters

Pull Request - State: closed - Opened by arahuja over 8 years ago - 3 comments

#604 - add PartitionReads cmd

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#603 - add `partition-loci` cmd

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#602 - ReferenceBroadcast improvements

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#601 - fix DeBruijnGraph filename typo

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#600 - fold AffineGapPenaltyAlignment into ReadAlignment

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#599 - remove method-access boilerplate

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#598 - allow spark confs as cmdline flags

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#597 - fold halfWindowSize into args plumbing

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#596 - rm ParRegArgs from ReadSets args

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#595 - LociPartitioning cleanups

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#594 - scala 2.11 forward-compat fixes and misc build tweaks

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#593 - use coarser loci-ranges in TakeLociIterator

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 6 comments

#592 - rm unused DebugLogArgs

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#591 - test-script refactor

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#590 - rm broken .array call

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 4 comments

#589 - lots of pom, shading, scripts improvements

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#588 - Can't use guacamole in spark-shell due to guava-shading nuances

Issue - State: closed - Opened by ryan-williams over 8 years ago
Labels: bug, help wanted

#587 - improvements / bugfix in capped-regions partitioner

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#586 - shade breeze

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#585 - Breeze NoSuchMethodError

Issue - State: closed - Opened by ryan-williams over 8 years ago - 9 comments
Labels: bug

#584 - bump shade plugin version, fix assembly build

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#583 - Error when packaging uber jar

Issue - State: closed - Opened by e5c over 8 years ago

#582 - port POM to org.hammerlab:scala-parent-pom

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#581 - "upgrade" adam to forked "0.20.0"

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 8 comments

#580 - rm "-fasta" from reference-param name

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 4 comments

#579 - Scripts overhaul

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 6 comments

#578 - Merge master into hbupgrade, resolving conflicts, and add a couple things

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 3 comments

#577 - Move commons-io back to standard dep

Pull Request - State: closed - Opened by arahuja over 8 years ago - 1 comment

#576 - add somatic-standard end-to-end test

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 4 comments

#575 - Fix ordering of tumor and normal read data

Pull Request - State: closed - Opened by arahuja over 8 years ago - 6 comments

#574 - likelihood nits

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 2 comments

#573 - logging nits

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 1 comment

#572 - throwed exception: ./scripts/guacamole: line 39 :exec: time: not found

Issue - State: open - Opened by car2008 over 8 years ago - 27 comments

#571 - Update likelihood code to handle non-uniform allelic mixtures

Pull Request - State: closed - Opened by arahuja over 8 years ago - 4 comments

#570 - Move logging to grizzled slf4j

Pull Request - State: closed - Opened by arahuja over 8 years ago - 3 comments

#569 - Upgrade Hadoop BAM for better interval filtering

Pull Request - State: closed - Opened by arahuja over 8 years ago - 7 comments

#568 - Move likelihood code to breeze

Pull Request - State: closed - Opened by arahuja over 8 years ago - 19 comments

#567 - Revert somatic standard tests to use table properties

Pull Request - State: closed - Opened by arahuja over 8 years ago - 2 comments

#566 - Move to Spark 2.0

Issue - State: open - Opened by arahuja over 8 years ago - 2 comments

#565 - correct tumorl to tumor

Pull Request - State: closed - Opened by arahuja over 8 years ago - 2 comments

#564 - travis scoverage attempt

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 10 comments

#563 - upgrade to magic-rdds 1.0.0

Pull Request - State: closed - Opened by ryan-williams over 8 years ago

#562 - fix broken docstring

Pull Request - State: closed - Opened by ryan-williams over 8 years ago

#561 - truncate progress-printing of LociPartitioning

Pull Request - State: closed - Opened by ryan-williams over 8 years ago

#560 - Send relevant reference sequences to executors in more fine-grained ways than via a Broadcast

Issue - State: open - Opened by ryan-williams over 8 years ago
Labels: infrastructure

#559 - add scripts for printing JAR paths, classpath

Pull Request - State: closed - Opened by ryan-williams over 8 years ago

#553 - Allow receiving inputs from config files

Issue - State: open - Opened by ryan-williams over 8 years ago
Labels: infrastructure

#551 - Remove `progress` helper, use Spark/log4j

Issue - State: open - Opened by ryan-williams over 8 years ago
Labels: enhancement, infrastructure

#548 - Test running on Baylor "case 2" dataset

Issue - State: open - Opened by ryan-williams over 8 years ago - 2 comments
Labels: validation

#539 - Parends nits

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 6 comments

#523 - expand some blocks over more lines for legibility

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 4 comments

#512 - Allow reference file to be loaded from HDFS or GS

Issue - State: open - Opened by arahuja over 8 years ago
Labels: infrastructure

#502 - VAFHistogram/VariantSupport: handle multiple samples in one RDD pipeline

Pull Request - State: closed - Opened by ryan-williams over 8 years ago - 4 comments

#494 - Use Maven dependency plugin to generate classpath of transitive dependencies

Issue - State: closed - Opened by ryan-williams over 8 years ago
Labels: enhancement

#476 - Save loci partitioning to a file instead of printing to screen

Issue - State: closed - Opened by arahuja almost 9 years ago - 1 comment

#474 - Audit/Reduce repo size

Issue - State: closed - Opened by ryan-williams almost 9 years ago
Labels: enhancement, infrastructure

#450 - Update description to account for dropped caller

Issue - State: closed - Opened by e5c almost 9 years ago

#447 - consider supporting other output formats (csv, json, arrow?) in joint caller

Issue - State: open - Opened by timodonnell almost 9 years ago - 2 comments
Labels: infrastructure

#442 - Ensure VCFs comply with the VCFv4.1 spec

Issue - State: open - Opened by e5c almost 9 years ago
Labels: infrastructure

#439 - Codify style rules

Issue - State: open - Opened by ryan-williams almost 9 years ago - 7 comments
Labels: infrastructure

#438 - Upgrade to Scala 2.11

Issue - State: open - Opened by ryan-williams almost 9 years ago - 5 comments
Labels: infrastructure

#433 - Upgrade Hadoop BAM to use BAM index

Pull Request - State: closed - Opened by arahuja almost 9 years ago - 4 comments

#424 - support writing Guacamole commands in separate projects

Issue - State: open - Opened by timodonnell almost 9 years ago - 2 comments
Labels: infrastructure

#402 - Allow for reading in block gzip compressed VCF files.

Issue - State: open - Opened by jstjohn almost 9 years ago - 2 comments
Labels: infrastructure

#399 - Upgrade HadoopBAM to use BAM index

Issue - State: closed - Opened by arahuja almost 9 years ago
Labels: infrastructure

#390 - joint caller: use phasing information for better calls

Issue - State: open - Opened by timodonnell almost 9 years ago
Labels: variant calling

#389 - joint caller: output phasing information

Issue - State: open - Opened by timodonnell almost 9 years ago - 1 comment
Labels: variant calling

#385 - joint caller: implement filters

Issue - State: open - Opened by timodonnell about 9 years ago - 3 comments
Labels: variant calling

#383 - Investigate filtering reads on load using HadoopBAM

Issue - State: closed - Opened by arahuja about 9 years ago - 1 comment
Labels: infrastructure

#370 - Ensure test BAM files are valid

Issue - State: open - Opened by hammer about 9 years ago - 2 comments
Labels: validation

#365 - Properly handle CIGAR P element

Issue - State: open - Opened by arahuja over 9 years ago
Labels: infrastructure

#352 - exclude clipped reads from pileups

Issue - State: open - Opened by timodonnell over 9 years ago - 3 comments
Labels: infrastructure

#329 - Move back to multi-module project

Issue - State: open - Opened by arahuja over 9 years ago - 3 comments
Labels: infrastructure

#319 - call CNVs even in exome data by finding change points in tumor/normal depth ratio

Issue - State: open - Opened by timodonnell over 9 years ago
Labels: variant calling

#298 - Potential mapping error filter

Issue - State: open - Opened by hammer over 9 years ago
Labels: variant calling

#296 - Add ability to filter to PASS variants in ReadEvidence

Issue - State: open - Opened by arahuja over 9 years ago
Labels: validation

#295 - Purity estimation for variant calling

Issue - State: open - Opened by arahuja over 9 years ago
Labels: variant calling

#254 - Investigate size of broadcast variable

Issue - State: open - Opened by arahuja about 10 years ago - 2 comments
Labels: infrastructure

#244 - add coveralls support

Issue - State: closed - Opened by timodonnell over 10 years ago
Labels: infrastructure

#217 - write out a VCF file instead of a VCF directory with a part-0000 file

Issue - State: open - Opened by timodonnell over 10 years ago - 2 comments
Labels: infrastructure

#205 - Add comments and tests for Filters package

Issue - State: open - Opened by timodonnell over 10 years ago
Labels: variant calling

#137 - Make test SAM file generation reproducible and document how/why each was created

Issue - State: open - Opened by arahuja over 10 years ago
Labels: validation

#135 - QualityAlignedReadsFilter is wasteful and hurts read/task distribution

Issue - State: closed - Opened by arahuja over 10 years ago
Labels: enhancement, help wanted

#131 - Structural variant output

Issue - State: closed - Opened by arahuja over 10 years ago

#125 - Emit Structural Variants

Issue - State: closed - Opened by ryan-williams over 10 years ago

#124 - Apply assembly algorithms to variant-heavy regions

Issue - State: open - Opened by ryan-williams over 10 years ago - 1 comment
Labels: variant calling

#121 - Investigate possible microbenchmark utilities

Issue - State: open - Opened by arahuja over 10 years ago
Labels: validation

GitHub / hammerlab/guacamole issues and pull requests