ADAM 0.16.0 is now available.

This release improves the performance of Base Quality Score Recalibration (BQSR) by 3.5x, adds support for multiline FASTQ input, visualization of variants when given VCF input, includes a new RegionJoin implementation that is shuffle-based, and adds new methods for region coverage calculations.

Drop into our Gitter channel to talk with us about this release


Complete list of changes for ADAM 0.16.0:

  • ISSUE 570: A few small conversion fixes
  • ISSUE 579: [ADAM-578] Update end of read when trimming.
  • ISSUE 564: [ADAM-563] Add warning message when saving Parquet files with incorrect extension
  • ISSUE 576: Changed hashCode implementations to improve performance of BQSR
  • ISSUE 569: Typo in the narrowPeak parser
  • ISSUE 568: Moved the Timers object from bdg-utils back to ADAM
  • ISSUE 478: Move non-genomics code
  • ISSUE 550: [ADAM-549] Added documentation for testing and CI for ADAM.
  • ISSUE 555: Makes maybeLoadVCF private.
  • ISSUE 558: Makes Features2ADAMSuite use SparkFunSuite
  • ISSUE 557: Randomize ports and turn off Spark UI to reduce bind exceptions in tests
  • ISSUE 552: Create test suite for FlagStat
  • ISSUE 554: privatize ADAMContext.maybeLoad{Bam,Fastq}
  • ISSUE 551: [ADAM-386] Multiline FASTQ input
  • ISSUE 542: Variants Visualization
  • ISSUE 545: [ADAM-543][ADAM-544] Fix issues with ADAM scripts and classpath
  • ISSUE 535: [ADAM-441] put a check in for Nothing. Throws an IAE if no return type is provided
  • ISSUE 546: [ADAM-532] Fix wigFix intermittent test failure
  • ISSUE 534: [ADAM-528][ADAM-533] Adds new RegionJoin impl that is shuffle-based
  • ISSUE 531: [ADAM-529] Attaching scaladoc to released distribution.
  • ISSUE 413: [ADAM-409][ADAM-520] Added local wigfix2bed tool
  • ISSUE 527: [ADAM-526] VcfAnnotation2ADAM only counts once
  • ISSUE 523: don’t open non-.adam-extension files as ADAM files
  • ISSUE 521: quieting wget output
  • ISSUE 482: [ADAM-462] Coverage region calculation
  • ISSUE 515: [ADAM-510] fix for bash syntax error; add ADDL_JARS check to adam-submit