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1 | 1 | # ADAM Changelog # |
2 | 2 |
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| 3 | +### Version 0.37.0 ### |
| 4 | + |
| 5 | +**Closed issues:** |
| 6 | + |
| 7 | + - error when saveAsPairedFastq files [\#2350](https://github.com/bigdatagenomics/adam/issues/2350) |
| 8 | + - Note Bioconda and Homebrew in readme and installation docs [\#2348](https://github.com/bigdatagenomics/adam/issues/2348) |
| 9 | + - Migrate Github Actions JDK from 'adopt' to 'temurin' [\#2346](https://github.com/bigdatagenomics/adam/issues/2346) |
| 10 | + - Update pom.xml url to Github repository [\#2342](https://github.com/bigdatagenomics/adam/issues/2342) |
| 11 | + - Update bdg-formats to 0.17.0 release [\#2341](https://github.com/bigdatagenomics/adam/issues/2341) |
| 12 | + - Note Spark version 3.2.0 or later is now required [\#2339](https://github.com/bigdatagenomics/adam/issues/2339) |
| 13 | + - Update Parquet to 1.12.x, Avro to 1.10.x, remove build workarounds [\#2336](https://github.com/bigdatagenomics/adam/issues/2336) |
| 14 | + - Extract multi region in one shot [\#2334](https://github.com/bigdatagenomics/adam/issues/2334) |
| 15 | + - Add proteinId field to Feature [\#2333](https://github.com/bigdatagenomics/adam/issues/2333) |
| 16 | + - Update Spark dependency version to 3.2.0 [\#2331](https://github.com/bigdatagenomics/adam/issues/2331) |
| 17 | + - Missing SAM header when using pipe API [\#2322](https://github.com/bigdatagenomics/adam/issues/2322) |
| 18 | + - saveAsSam format [\#2321](https://github.com/bigdatagenomics/adam/issues/2321) |
| 19 | + - Remove Github Pages environment and branch [\#2313](https://github.com/bigdatagenomics/adam/issues/2313) |
| 20 | + - ArrayIndexOutOfBoundsException when operating on VCF DataFrame doesn't indicate bad row [\#2275](https://github.com/bigdatagenomics/adam/issues/2275) |
| 21 | + - InMemoryFileIndex$SerializableFileStatus is not registered [\#2187](https://github.com/bigdatagenomics/adam/issues/2187) |
| 22 | + - Investigate registrator performance re classForName [\#2185](https://github.com/bigdatagenomics/adam/issues/2185) |
| 23 | + - Keep dataset transformations on datasets where appropriate [\#2166](https://github.com/bigdatagenomics/adam/issues/2166) |
| 24 | + - Code generate conversion functions from templates [\#2163](https://github.com/bigdatagenomics/adam/issues/2163) |
| 25 | + - Replace dependency on Hadoop-BAM with Disq [\#2111](https://github.com/bigdatagenomics/adam/issues/2111) |
| 26 | + - Explore alternatives for code generating Scala products and projections from Avro schema [\#2110](https://github.com/bigdatagenomics/adam/issues/2110) |
| 27 | + - Support for Elastic Search [\#2071](https://github.com/bigdatagenomics/adam/issues/2071) |
| 28 | + - loadIndexedBam pulls entire bam file on http files, even when predicate is specified [\#2057](https://github.com/bigdatagenomics/adam/issues/2057) |
| 29 | + - Add API docs where unmapped reads are discarded [\#2022](https://github.com/bigdatagenomics/adam/issues/2022) |
| 30 | + - Indel realignment discards all unmapped reads [\#2018](https://github.com/bigdatagenomics/adam/issues/2018) |
| 31 | + - NullPointerException at htsjdk CramNormalizer.getByteOrDefault [\#1993](https://github.com/bigdatagenomics/adam/issues/1993) |
| 32 | + - Add support for left semi, left anti region join [\#1990](https://github.com/bigdatagenomics/adam/issues/1990) |
| 33 | + - Alternate allele depth is incorrect for gVCF reference models [\#1987](https://github.com/bigdatagenomics/adam/issues/1987) |
| 34 | + - Add examples to all functions supported across languages [\#1962](https://github.com/bigdatagenomics/adam/issues/1962) |
| 35 | + - Log validation errors back to driver [\#1950](https://github.com/bigdatagenomics/adam/issues/1950) |
| 36 | + - Parallelize loading metadata [\#1902](https://github.com/bigdatagenomics/adam/issues/1902) |
| 37 | + - Release cycle on pypi [\#1888](https://github.com/bigdatagenomics/adam/issues/1888) |
| 38 | + - suffix arrays implementation [\#1872](https://github.com/bigdatagenomics/adam/issues/1872) |
| 39 | + - ArrayIndexOutOfBoundsException in AbstractVCFCodec.oneAllele [\#1868](https://github.com/bigdatagenomics/adam/issues/1868) |
| 40 | + - Allow users to configure partitioning for pipe APIs [\#1863](https://github.com/bigdatagenomics/adam/issues/1863) |
| 41 | + - optimize SmithWaterman alignment [\#1850](https://github.com/bigdatagenomics/adam/issues/1850) |
| 42 | + - Support pushing down range queries to CRAM index [\#1833](https://github.com/bigdatagenomics/adam/issues/1833) |
| 43 | + - Exporting non-reference genotype likelihoods to VCF appears to fail for triploid sites [\#1776](https://github.com/bigdatagenomics/adam/issues/1776) |
| 44 | + - Reconstructing variant contexts will be incorrect if a variant has different qualities across samples [\#1773](https://github.com/bigdatagenomics/adam/issues/1773) |
| 45 | + - GenomicRDD.transform should allow preserving partitioning [\#1761](https://github.com/bigdatagenomics/adam/issues/1761) |
| 46 | + - Add ability to normalize INDEL variants [\#1710](https://github.com/bigdatagenomics/adam/issues/1710) |
| 47 | + - Inferred serializer for fast concatenation engine can stack overflow [\#1708](https://github.com/bigdatagenomics/adam/issues/1708) |
| 48 | + - Write out BAI when saving sorted BAMs to disk [\#1654](https://github.com/bigdatagenomics/adam/issues/1654) |
| 49 | + - Create bash completion file for adam-submit [\#1652](https://github.com/bigdatagenomics/adam/issues/1652) |
| 50 | + - Make it easier to modify/interrogate metadata from Python/R [\#1604](https://github.com/bigdatagenomics/adam/issues/1604) |
| 51 | + - Support ShuffleRegionJoins when an rdd is sorted by contig number [\#1519](https://github.com/bigdatagenomics/adam/issues/1519) |
| 52 | + - Clean up replicated join code in INDEL realigner and BQSR [\#1429](https://github.com/bigdatagenomics/adam/issues/1429) |
| 53 | + - Improve unit test coverage of Feature parser/encoder helper [\#1418](https://github.com/bigdatagenomics/adam/issues/1418) |
| 54 | + - Write unit tests for CLI [\#1416](https://github.com/bigdatagenomics/adam/issues/1416) |
| 55 | + - Write unit tests for ParquetFileTraversable [\#1415](https://github.com/bigdatagenomics/adam/issues/1415) |
| 56 | + - Add regression test suite [\#1407](https://github.com/bigdatagenomics/adam/issues/1407) |
| 57 | + - Address classes with lower than ideal coverage [\#1405](https://github.com/bigdatagenomics/adam/issues/1405) |
| 58 | + - Genotype filtersPassed field not set correctly [\#1269](https://github.com/bigdatagenomics/adam/issues/1269) |
| 59 | + - Need clear error messages when schema has backward-incompatible change [\#345](https://github.com/bigdatagenomics/adam/issues/345) |
| 60 | + - Annotate classes with their production worthiness [\#123](https://github.com/bigdatagenomics/adam/issues/123) |
| 61 | + |
| 62 | +**Merged and closed pull requests:** |
| 63 | + |
| 64 | + - Add conda, homebrew, biocontainers installation docs [\#2352](https://github.com/bigdatagenomics/adam/pull/2352) ([heuermh](https://github.com/heuermh)) |
| 65 | + - Migrate Github Actions JDK from 'adopt' to 'temurin' [\#2347](https://github.com/bigdatagenomics/adam/pull/2347) ([heuermh](https://github.com/heuermh)) |
| 66 | + - [ADAM-2341] Update bdg-formats dependency version to 0.17.0 [\#2345](https://github.com/bigdatagenomics/adam/pull/2345) ([heuermh](https://github.com/heuermh)) |
| 67 | + - [ADAM-2185] Reduce classForName calls to improve registrator performance [\#2344](https://github.com/bigdatagenomics/adam/pull/2344) ([heuermh](https://github.com/heuermh)) |
| 68 | + - Update pom.xml url to Github repository [\#2343](https://github.com/bigdatagenomics/adam/pull/2343) ([heuermh](https://github.com/heuermh)) |
| 69 | + - Update Scala dependency version to 2.12.15 [\#2340](https://github.com/bigdatagenomics/adam/pull/2340) ([heuermh](https://github.com/heuermh)) |
| 70 | + - [ADAM-2333] Add proteinId field to Feature [\#2338](https://github.com/bigdatagenomics/adam/pull/2338) ([heuermh](https://github.com/heuermh)) |
| 71 | + - Update github-changes-maven-plugin version to 1.2 [\#2337](https://github.com/bigdatagenomics/adam/pull/2337) ([heuermh](https://github.com/heuermh)) |
| 72 | + - Bump adam-python development version to 0.37.0a0 [\#2332](https://github.com/bigdatagenomics/adam/pull/2332) ([heuermh](https://github.com/heuermh)) |
| 73 | + - trim sam format readname [\#2325](https://github.com/bigdatagenomics/adam/pull/2325) ([hxdhan](https://github.com/hxdhan)) |
| 74 | + - Update Spark to 3.2.0, Parquet to 1.12.1, Avro to 1.10.2 [\#2289](https://github.com/bigdatagenomics/adam/pull/2289) ([heuermh](https://github.com/heuermh)) |
| 75 | + - Refactor Genotype and GenotypeAnnotation [\#2117](https://github.com/bigdatagenomics/adam/pull/2117) ([heuermh](https://github.com/heuermh)) |
| 76 | + - Keep information for <NON_REF> alleles [\#2116](https://github.com/bigdatagenomics/adam/pull/2116) ([karenfeng](https://github.com/karenfeng)) |
| 77 | + |
| 78 | + |
3 | 79 | ### Version 0.36.0 ### |
4 | 80 |
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5 | 81 | **Closed issues:** |
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