We’re proud to announce the release of ADAM 0.15.0!
This release includes important memory and performance improvements, better documentation, new features and many bug fixes.
We have upgraded from Parquet
1.6.0 in order to dramatically reduce our memory footprint. For string columns with dictionary encoding, the amount of memory used will now be proportional to the number of dictionary entries instead of the number of records materialized. Parquet 1.6.0 also provides improved column statistics and the ability to store custom metadata. We will use these features in subsequent ADAM releases to improve random access performance. Note that ADAM
0.14.0 had a serious memory regression so upgrading to
0.15.0 as soon as possible is recommended.
We are unhappy with the quality of the documentation we have been providing ADAM users and are working to improve it. With this release, all documentation has been centralized into the
./docs directory and we’re using
pandoc to convert the Markdown source into both PDF and HTML formats. We are committed to improving the content of the docs over time and welcome your pull requests!
This release includes binary distributions to make it easier for you to get up and running with ADAM. We do not include any Spark or Hadoop artifacts in order to prevent versioning conflicts. For application developers, we have also changed our Spark and Hadoop dependencies to
provided. This means that you can more easily running on ADAM using your preferred Spark and Hadoop version and configuration. We want to make deployment as easy as possible.
This release includes numerous features and bug fixes that are detailed below:
- ISSUE 509: Add a ‘distribution’ module to create assemblies
- ISSUE 508: Upgrade from Parquet 1.4.3 to 1.6.0rc4
- ISSUE 498: [ADAM-496] Changes VCF to flat ADAM command name and usage
- ISSUE 500: [ADAM-495] Require SPARK_HOME for adam-submit
- ISSUE 501: [ADAM-499] Add -onlyvariants option to vcf2adam
- ISSUE 507: [ADAM-505] Removed
- ISSUE 504: [ADAM-502] Add missing Long implicit to ColumnReaderInput
- ISSUE 503: [ADAM-473] Make RecordCondition and FieldCondition public
- ISSUE 494: Fix foreach block for vcf ingest
- ISSUE 492: Documentation cleanup and style improvements
- ISSUE 481: [ADAM-480] Switch assembly to single goal.
- ISSUE 487: [ADAM-486] Add port option to viz command.
- ISSUE 469: [ADAM-461] Fix ReferenceRegion and ReferencePosition impl
- ISSUE 440: [ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings
- ISSUE 470: added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions
- ISSUE 468: refactor RDD loading; explicitly load alignments
- ISSUE 474: Consolidate documentation into a single location in source.
- ISSUE 471: Fixed typo on MAVEN_OPTS quotation mark
- ISSUE 467: [ADAM-436] Optionally output original qualities to fastq
- ISSUE 451: add
adam viewcommand, analogous to
- ISSUE 466: working examples on .sam included in repo
- ISSUE 458: Remove unused val from Reads2Ref
- ISSUE 438: Add ability to save paired-FASTQ files
- ISSUE 457: A few random Predicate-related cleanups
- ISSUE 459: a few tweaks to scripts/jenkins-test
- ISSUE 460: Project only the sequence when kmer/qmer counting
- ISSUE 450: Refactor some file writing and reading logic
- ISSUE 455: [ADAM-454] Add serializers for Avro objects which don’t have serializers
- ISSUE 447: Update the contribution guidelines
- ISSUE 453: Better null handling for isSameContig utility
- ISSUE 417: Stores original position and original cigar during realignment.
- ISSUE 449: read “OQ” attr from structured SAMRecord field
- ISSUE 446: Revert “[ADAM-237] Migrate to Chill serialization libraries.”
- ISSUE 437: random nits
- ISSUE 434: Few transform tweaks
- ISSUE 435: [ADAM-403] Remove seqDict from RegionJoin
- ISSUE 431: A few tweaks, typo corrections, and random cleanups
- ISSUE 430: [ADAM-429] adam-submit now handles args correctly.
- ISSUE 427: Fixes for indel realigner issues
- ISSUE 418: [ADAM-416] Removing ‘ADAM’ prefix
- ISSUE 404: [ADAM-327] Adding gene, transcript, and exon models.
- ISSUE 414: Fix error in
- ISSUE 415: Update README.md to reflect Spark 1.1
- ISSUE 412: [ADAM-411] Updated usage aliases in README. Fixes #411.
- ISSUE 408: [ADAM-405] Add FASTQ output.
- ISSUE 385: [ADAM-384] Adds import from FASTQ.
- ISSUE 400: [ADAM-399] Fix link to schemas.
- ISSUE 396: [ADAM-388] Sets Kryo serialization with —conf args
- ISSUE 394: [ADAM-393] Adds knobs to SparkContext creation in SparkFunSuite
- ISSUE 391: [ADAM-237] Migrate to Chill serialization libraries.
- ISSUE 380: Rewrite of MarkDuplicates which seems to improve performance
- ISSUE 387: fix some deprecation warnings