The 0.17.0 release of ADAM includes a release for Scala 2.10 and a release for Scala 2.11. We’ve been working to cleanup APIs and simplify ADAM for developers. Code that isn’t useful has been removed. Code that belongs in other downstream or upstream projects has been moved. Parquet and HTSJDK has been upgraded.
There are also some new features, e.g. you can now now
transform all the SAM/BAM files in a directory by specifying the directory and there’s a new
flatten command that allows you to flatten the schema of ADAM data to process in Impala, Hive, SparkSQL, etc; there are also many bug fixes.
For more details, see the following pull requests:
- ISSUE 691: fix BAM/SAM header setting when writing on cluster
- ISSUE 688: make adamLoad public
- ISSUE 694: Fix parent reference in distribution module
- ISSUE 684: a few region-join nits
- ISSUE 682: [ADAM-681] Remove menacing error message about reqd .adam extension
- ISSUE 680: [ADAM-674] Delete Bam2ADAM.
- ISSUE 678: upgrade to bdg utils 0.2.1
- ISSUE 668: [ADAM-597] Move correction out of ADAM and into a downstream project.
- ISSUE 671: Bug fix in ReferenceUtils.unionReferenceSet
- ISSUE 667: [ADAM-666] Clean up key not found error in partitioner code.
- ISSUE 656: Update Vcf2ADAM.scala
- ISSUE 652: added filterByOverlappingRegion in GeneFeatureRDDFunctions
- ISSUE 650: [ADAM-649] Support transform of all BAM/SAM files in a directory.
- ISSUE 647: [ADAM-646] Special case reads with ‘*’ quality during BQSR.
- ISSUE 645: [ADAM-634] Create a local ParquetLister for testing purposes.
- ISSUE 633: [Adam] Tests for SAMRecordConverter.scala
- ISSUE 641: [ADAM-640] Fix incorrect exclusion for org.seqdoop.htsjdk.
- ISSUE 632: [ADAM-631] Allow VCF conversion to sort on output after coalescing.
- ISSUE 628: [ADAM-627] Makes ReferenceFile trait extend Serializable.
- ISSUE 637: check for mac brew alternate spark install structure
- ISSUE 624: Conceptual fix for duplicate marking and sorting stragglers
- ISSUE 629: [ADAM-604] Remove normalization code.
- ISSUE 630: Add flatten command.
- ISSUE 619: [ADAM-540] Move to new HTSJDK release; should support Java 8.
- ISSUE 626: [ADAM-625] Enable globbing for BAM.
- ISSUE 621: Removes the predicates package.
- ISSUE 620: [ADAM-600] Adding RegionJoin trait.
- ISSUE 616: [ADAM-565] Upgrade to Parquet filter2 API.
- ISSUE 613: [ADAM-612] Point to proper k-mer counters.
- ISSUE 588: [ADAM-587] Clean up loading checks.
- ISSUE 592: [ADAM-513] Remove ReferenceMappable trait.
- ISSUE 606: [ADAM-605] Remove visualization code.
- ISSUE 596: [ADAM-595] Delete the ‘comparisons’ code.
- ISSUE 590: [ADAM-589] Removed pileup code.
- ISSUE 586: [ADAM-452] Fixes SM attribute on ADAM to BAM conversion.
- ISSUE 584: [ADAM-583] Add k-mer counting functionality for nucleotide contig fragments