bigdatagenomics/cannoli

Issues

• Update Spark dependency version to 3.3.2

  #357 opened 2 years ago by heuermh
  0

• Interest in multisample freebayes calling

  #352 opened 2 years ago by colindaven
  14

• Update Spark dependency version to 3.3.1

  #354 opened 2 years ago by heuermh
  0

• Update Spark dependency version to 3.3.0

  #351 opened 2 years ago by heuermh
  1

• Update ADAM dependency version to 1.0

  #349 opened 3 years ago by heuermh
  0

• Find bwa singularity image for README example

  #347 opened 3 years ago by heuermh
  0

• Consider refactoring for single end, paired end, long reads

  #326 opened 3 years ago by heuermh
  1

• BWA aln

  #323 opened 3 years ago by yassineS
  9

• Update ADAM dependency version to 0.37.0

  #340 opened 3 years ago by heuermh
  0

• Migrate Github Actions JDK from 'adopt' to 'temurin'

  #337 opened 3 years ago by heuermh
  0

• BWA MEM yields an empty alignment

  #324 opened 3 years ago by yassineS
  10

• Update ADAM dependency version to 0.36.0

  #321 opened 3 years ago by heuermh
  0

• Update minimap2 to version 2.22

  #319 opened 3 years ago by heuermh
  0

• Update minimap2 to version 2.20

  #313 opened 3 years ago by heuermh
  0

• Update Spark dependency version to 3.1.2

  #311 opened 3 years ago by heuermh
  0

• Update Spark dependency version to 3.1.1

  #292 opened 4 years ago by heuermh
  0

• Add support for single end (.fq) and long reads (.fa) for minimap2/unimap

  #306 opened 4 years ago by heuermh
  0

• Set build status on GitHub commit [deprecated] changed build result to FAILURE

  #293 opened 4 years ago by heuermh
  0

• Migrate CI off Jenkins

  #297 opened 4 years ago by heuermh
  0

• Add CRAM reference argument for loading alignments and fragments

  #287 opened 4 years ago by heuermh
  0

• Cannoli on Spark

  #276 opened 4 years ago by tahashmi
  3

• Default build to Hadoop 3.x

  #283 opened 4 years ago by heuermh
  0

• Bump Scala 2.12 dependency version to 2.12.10

  #280 opened 4 years ago by heuermh
  0

• Remove Spark 2.x from build and release matrix

  #281 opened 4 years ago by heuermh
  0

• Remove Scala 2.11.x from build and release matrix

  #282 opened 4 years ago by heuermh
  0

• Release artifacts for version 0.11.0 are incorrect

  #284 opened 4 years ago by heuermh
  0

• Bump ADAM dependency version to 0.33.0

  #278 opened 4 years ago by heuermh
  0

• Can not run vep

  #244 opened 4 years ago by toanddt
  13

• BwaArgs is not a member of package org.bdgenomics.cannoli

  #274 opened 4 years ago by tahashmi
  7

• java.lang.UnsupportedOperationException: empty.max while sorting and indexing.

  #237 opened 4 years ago by Arun-George-Zachariah
  5

• force evaluating accumulators before assigning them

  #243 opened 5 years ago by yvanst
  3

• conda install cannoli issue

  #268 opened 4 years ago by tahashmi
  2

• Exception encountered while loading parquet files generated using Cannoli CLI.

  #258 opened 4 years ago by Arun-George-Zachariah
  3

• Issue while saving variants as vcf.

  #260 opened 4 years ago by Arun-George-Zachariah
  8

• IllegalArgumentException: Reference index for 'chr3' not found in sequence dictionary

  #236 opened 4 years ago by Arun-George-Zachariah
  8

• Add additional arguments for freebayes command line wrapper

  #271 opened 4 years ago by heuermh
  0

• Trying to install/run on HPC using Singularity

  #238 opened 4 years ago by moldach
  5

• Refactor variant callers to fn[AlignmentDataset, GenotypeDataset]

  #272 opened 4 years ago by heuermh
  1

• Update Spark dependency to version 3.0.1

  #265 opened 4 years ago by heuermh
  0

• Refactor Bwa class names to BwaMem

  #257 opened 4 years ago by heuermh
  0

• Add bwa-mem2 for aligning fragments

  #255 opened 4 years ago by heuermh
  0

• Default build to Spark 3/Scala 2.12

  #248 opened 4 years ago by heuermh
  0

• Update ADAM dependency version to 0.32.0

  #252 opened 4 years ago by heuermh
  0

• Update Spark dependency version to 2.4.6

  #245 opened 4 years ago by heuermh
  0

• Unable to find bowtie2 index from hdfs

  #246 opened 4 years ago by dnl-rss
  3

• Use biocontainers as default container image for vt

  #241 opened 5 years ago by heuermh
  0

• Freebayes CLI command writes to wrong path

  #239 opened 5 years ago by yvanst
  1

• Update ADAM dependency version to 0.31.0

  #233 opened 5 years ago by heuermh
  0

• bowtie2 empty output

  #229 opened 5 years ago by yvanst
  2

• Bowtie2 2.3.5 does not work with --interleaved option

  #228 opened 5 years ago by heuermh
  0