Issues

• ArrayList cannot be cast to class String in VariantContextConverter

  bigdatagenomics/adam#2419 · Filter by author heuermh opened on Jun 26, 2025

• Update Spark dependency version to 4.x

  bigdatagenomics/adam#2418 · Filter by author heuermh opened on Jun 26, 2025

• Refactoring Error Logging Inconsistencies in MdTag.scala

  bigdatagenomics/adam#2401 · Filter by author joonkang-git opened on Aug 2, 2024 · 1.0.2

• Missing Fastq reads

  bigdatagenomics/adam#2385 · Filter by author SidWeng opened on Mar 24, 2023
  1

• StackOverflowError in avro SpecificDatumWriter

  bigdatagenomics/adam#2349 · Filter by author heuermh opened on Nov 29, 2021
  1

• Add Scala 2.13 to build

  bigdatagenomics/adam#2335 · Filter by author heuermh opened on Oct 12, 2021

• Spare not needed groupBy when calling toFragments() on AlignmentDataset

  bigdatagenomics/adam#2281 · Filter by author benraha opened on Nov 7, 2020
  4

• Improve Ensembl VEP mapping to TranscriptEffect

  bigdatagenomics/adam#2279 · Filter by author heuermh opened on Oct 28, 2020
  1

• saveAsSam converts null mapping qualities to 0 instead of 255

  bigdatagenomics/adam#2272 · Filter by author heuermh opened on Sep 4, 2020

• I'm failing to use this package

  bigdatagenomics/adam#2225 · Filter by author Hoeze opened on Oct 10, 2019
  11

• Save as CRAM precondition incorrectly fails on sorted Parquet input

  bigdatagenomics/adam#2214 · Filter by author heuermh opened on Sep 25, 2019

• Refactor Dataset save methods for consistency

  bigdatagenomics/adam#2199 · Filter by author heuermh opened on Aug 26, 2019
  2

• Add missing VariantContextDataset.save method

  bigdatagenomics/adam#2198 · Filter by author heuermh opened on Aug 26, 2019

• Ensembl Variant Effect Predictor annotations support

  bigdatagenomics/adam#2150 · Filter by author znikasz opened on May 14, 2019
  3

• API doc links in readthedocs are broken

  bigdatagenomics/adam#2131 · Filter by author akmorrow13 opened on Feb 25, 2019
  3

• TypeError: 'JavaPackage' object is not callable

  bigdatagenomics/adam#2122 · Filter by author Shekharrajak opened on Feb 19, 2019
  13

• s3a URL not working

  bigdatagenomics/adam#2096 · Filter by author dekinsitro opened on Dec 5, 2018
  5

• Evenly Repartioning AlignmentRecordRDD fails with IllegalArgumentException on sorted RDD

  bigdatagenomics/adam#2063 · Filter by author pauldwolfe opened on Oct 11, 2018
  1

• Cannot run pyadam adam-distribution-spark2_2.11-0.24.0 binary distribution

  bigdatagenomics/adam#2041 · Filter by author asdf1234-deleted opened on Aug 31, 2018
  4

• Mark Duplicates implemented in Spark SQL

  bigdatagenomics/adam#2023 · Filter by author jondeaton opened on Jul 27, 2018

• Python/R pipe APIs return wrong GenomicRDD type

  bug
  bigdatagenomics/adam#2012 · Filter by author fnothaft opened on Jul 6, 2018
  

• Startup scripts still don't resolve correctly when symlinks

  bigdatagenomics/adam#1973 · Filter by author heuermh opened on Mar 28, 2018

• Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

  bigdatagenomics/adam#1956 · Filter by author heuermh opened on Mar 17, 2018
  3

• Timeout waiting for connection from pool for 1000 genomes vcf on AWS

  bigdatagenomics/adam#1951 · Filter by author akmorrow13 opened on Mar 11, 2018
  9

• Support loadIndexedBam from R

  enhancement
  bigdatagenomics/adam#1947 · Filter by author fnothaft opened on Mar 7, 2018