Modifying changelog.

bigdatagenomics · Jan 6, 2017 · da1d3a5 · da1d3a5
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 # ADAM #
 
+### Version 0.21.0 ###
+
+**Closed issues:**
+
+- Update Markdown docs with ValidationStringency in VCF<->ADAM CLI [\#1342](https://github.com/bigdatagenomics/adam/issues/1342)
+- Variant VCFHeaderLine metadata does not handle wildcards properly [\#1339](https://github.com/bigdatagenomics/adam/issues/1339)
+- Close called multiple times on VCF header stream [\#1337](https://github.com/bigdatagenomics/adam/issues/1337)
+- BroadcastRegionJoin has serialization failures [\#1334](https://github.com/bigdatagenomics/adam/issues/1334)
+- adam-cli uses git-commit-id-plugin which breaks release? [\#1322](https://github.com/bigdatagenomics/adam/issues/1322)
+- move_to_xyz scripts should have interlocks... [\#1317](https://github.com/bigdatagenomics/adam/issues/1317)
+- Lineage for partitionAndJoin in ShuffleRegionJoin causes StackOverflow Errors [\#1308](https://github.com/bigdatagenomics/adam/issues/1308)
+- Add move_to_spark_1.sh script and update README to mention [\#1307](https://github.com/bigdatagenomics/adam/issues/1307)
+- adam-submit transform fails with Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class [\#1306](https://github.com/bigdatagenomics/adam/issues/1306)
+- private ADAMContext constructor? [\#1296](https://github.com/bigdatagenomics/adam/issues/1296)
+- AlignmentRecord.mateAlignmentEnd never set [\#1290](https://github.com/bigdatagenomics/adam/issues/1290)
+- how to submit my own driver class via adam-submit? [\#1289](https://github.com/bigdatagenomics/adam/issues/1289)
+- ReferenceRegion on Genotype seems busted? [\#1286](https://github.com/bigdatagenomics/adam/issues/1286)
+- Clarify strandedness in ReferenceRegion apply methods [\#1285](https://github.com/bigdatagenomics/adam/issues/1285)
+- Parquet and CRAM debug logging during unit tests [\#1280](https://github.com/bigdatagenomics/adam/issues/1280)
+- Add more ANN field parsing unit tests [\#1273](https://github.com/bigdatagenomics/adam/issues/1273)
+- loadVariantAnnotations returns empty RDD [\#1271](https://github.com/bigdatagenomics/adam/issues/1271)
+- Implement joinVariantAnnotations with region join [\#1259](https://github.com/bigdatagenomics/adam/issues/1259)
+- Count how many chromosome in the range of the kmer [\#1249](https://github.com/bigdatagenomics/adam/issues/1249)
+- ADAM minor release to support htsjdk 2.7.0? [\#1248](https://github.com/bigdatagenomics/adam/issues/1248)
+- how to config kryo.registrator programmatically [\#1245](https://github.com/bigdatagenomics/adam/issues/1245)
+- Does the nested record Flattener drop Maps/Arrays? [\#1244](https://github.com/bigdatagenomics/adam/issues/1244)
+- Dead-ish code cleanup in `org.bdgenomics.adam.utils` [\#1242](https://github.com/bigdatagenomics/adam/issues/1242)
+- java.io.FileNotFoundException for old adam file after upgrade to adam0.20 [\#1240](https://github.com/bigdatagenomics/adam/issues/1240)
+- please add maven-source-plugin into the pom file [\#1239](https://github.com/bigdatagenomics/adam/issues/1239)
+- Assembly jar doesn't get rebuilt on CLI changes [\#1238](https://github.com/bigdatagenomics/adam/issues/1238)
+- how to compare with the last the column for the same chromosome name? [\#1237](https://github.com/bigdatagenomics/adam/issues/1237)
+- Need a way for users to add VCF header lines [\#1233](https://github.com/bigdatagenomics/adam/issues/1233)
+- Enhancements to VCF save [\#1232](https://github.com/bigdatagenomics/adam/issues/1232)
+- Must we split multi-allelic sites in our Genotype model? [\#1231](https://github.com/bigdatagenomics/adam/issues/1231)
+- Can't override default -collapse in reads2coverage [\#1228](https://github.com/bigdatagenomics/adam/issues/1228)
+- Reads2coverage NPEs on unmapped reads [\#1227](https://github.com/bigdatagenomics/adam/issues/1227)
+- Strand bias doesn't get exported [\#1226](https://github.com/bigdatagenomics/adam/issues/1226)
+- Move ADAMFunSuite helper functions upstream to SparkFunSuite [\#1225](https://github.com/bigdatagenomics/adam/issues/1225)
+- broadcast join using interval tree [\#1224](https://github.com/bigdatagenomics/adam/issues/1224)
+- Instrumentation is lost in ShuffleRegionJoin [\#1222](https://github.com/bigdatagenomics/adam/issues/1222)
+- Bump Spark, Scala, Hadoop dependency versions [\#1221](https://github.com/bigdatagenomics/adam/issues/1221)
+- GenomicRDD shuffle region join passes partition count to partition size [\#1220](https://github.com/bigdatagenomics/adam/issues/1220)
+- Scala compile errors downstream of Spark 2 Scala 2.11 artifacts [\#1218](https://github.com/bigdatagenomics/adam/issues/1218)
+- Javac error: incompatible types: SparkContext cannot be converted to ADAMContext [\#1217](https://github.com/bigdatagenomics/adam/issues/1217)
+- Release 0.20.0 artifacts failed Sonatype Nexus validation [\#1212](https://github.com/bigdatagenomics/adam/issues/1212)
+- Release script failed for 0.20.0 release [\#1211](https://github.com/bigdatagenomics/adam/issues/1211)
+- gVCF - can't load multi-allelic sites [\#1202](https://github.com/bigdatagenomics/adam/issues/1202)
+- Allow open-ended intervals in loadIndexedBam [\#1196](https://github.com/bigdatagenomics/adam/issues/1196)
+- Interval tree join in ADAM [\#1171](https://github.com/bigdatagenomics/adam/issues/1171)
+- spark-submit throw exception in spark-standalone using .adam which transformed from .vcf [\#1121](https://github.com/bigdatagenomics/adam/issues/1121)
+- BroadcastRegionJoin is not a broadcast join [\#1110](https://github.com/bigdatagenomics/adam/issues/1110)
+- Improve test coverage of VariantContextConverter [\#1107](https://github.com/bigdatagenomics/adam/issues/1107)
+- Variant dbsnp rs id tracking in vcf2adam and ADAM2Vcf [\#1103](https://github.com/bigdatagenomics/adam/issues/1103)
+- Document core ADAM transform methods [\#1085](https://github.com/bigdatagenomics/adam/issues/1085)
+- Document deploying ADAM on Toil [\#1084](https://github.com/bigdatagenomics/adam/issues/1084)
+- Clean up packages [\#1083](https://github.com/bigdatagenomics/adam/issues/1083)
+- VariantCallingAnnotations is getting populated with INFO fields [\#1063](https://github.com/bigdatagenomics/adam/issues/1063)
+- How to load DatabaseVariantAnnotation information ? [\#1049](https://github.com/bigdatagenomics/adam/issues/1049)
+- Release ADAM version 0.20.0 [\#1048](https://github.com/bigdatagenomics/adam/issues/1048)
+- Support VCF annotation ANN field in vcf2adam and adam2vcf [\#1044](https://github.com/bigdatagenomics/adam/issues/1044)
+- How to create a rich(er) VariantContext RDD? Reconstruct VCF INFO fields. [\#878](https://github.com/bigdatagenomics/adam/issues/878)
+- Add biologist targeted section to the README [\#497](https://github.com/bigdatagenomics/adam/issues/497)
+- Update usage docs running for EC2 and CDH [\#493](https://github.com/bigdatagenomics/adam/issues/493)
+- Add docs about building downstream apps on top of ADAM [\#291](https://github.com/bigdatagenomics/adam/issues/291)
+- Variant filter representation [\#194](https://github.com/bigdatagenomics/adam/issues/194)
+
+**Merged and closed pull requests:**
+
+- [ADAM-1342] Update CLI docs after #1288 merged. [\#1343](https://github.com/bigdatagenomics/adam/pull/1343) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1334] Clean up serialization issues in Broadcast region join. [\#1336](https://github.com/bigdatagenomics/adam/pull/1336) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1339] Use glob-safe method to load VCF header metadata for Parquet [\#1340](https://github.com/bigdatagenomics/adam/pull/1340) ([fnothaft](https://github.com/fnothaft))
+- Clean rewrite of VariantContextConverter [\#1288](https://github.com/bigdatagenomics/adam/pull/1288) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1337] Remove os.{flush,close} calls after writing VCF header. [\#1338](https://github.com/bigdatagenomics/adam/pull/1338) ([fnothaft](https://github.com/fnothaft))
+- HBase backend for Genotypes [\#1246](https://github.com/bigdatagenomics/adam/pull/1246) ([jpdna](https://github.com/jpdna))
+- HBase as a separate repo [\#1293](https://github.com/bigdatagenomics/adam/pull/1293) ([jpdna](https://github.com/jpdna))
+- Add interlocks for move_to_xyz scripts. [\#1319](https://github.com/bigdatagenomics/adam/pull/1319) ([fnothaft](https://github.com/fnothaft))
+- Populate fields on VariantAnnotation [\#1283](https://github.com/bigdatagenomics/adam/pull/1283) ([heuermh](https://github.com/heuermh))
+- some style nits [\#1278](https://github.com/bigdatagenomics/adam/pull/1278) ([ryan-williams](https://github.com/ryan-williams))
+- [ADAM-1322] Skip git commit plugin if .git is missing. [\#1323](https://github.com/bigdatagenomics/adam/pull/1323) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1307] move_to_spark_2 fails after moving to scala 2.11. [\#1329](https://github.com/bigdatagenomics/adam/pull/1329) ([fnothaft](https://github.com/fnothaft))
+- unroll/optimize some JavaConversions [\#1326](https://github.com/bigdatagenomics/adam/pull/1326) ([ryan-williams](https://github.com/ryan-williams))
+- clean up *Join type-params/scaldocs [\#1325](https://github.com/bigdatagenomics/adam/pull/1325) ([ryan-williams](https://github.com/ryan-williams))
+- Supports access to indexed fa and fasta files [\#1320](https://github.com/bigdatagenomics/adam/pull/1320) ([akmorrow13](https://github.com/akmorrow13))
+- Clean up CLI operation categories and names, and add documentation for CLI [\#1274](https://github.com/bigdatagenomics/adam/pull/1274) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1307] Add script for moving to Spark 1. [\#1318](https://github.com/bigdatagenomics/adam/pull/1318) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1308] Fix stack overflow in join with custom iterator impl. [\#1315](https://github.com/bigdatagenomics/adam/pull/1315) ([fnothaft](https://github.com/fnothaft))
+- Update move_to_spark_2.sh [\#1316](https://github.com/bigdatagenomics/adam/pull/1316) ([creggian](https://github.com/creggian))
+- Why Adam? section added to README.md [\#1310](https://github.com/bigdatagenomics/adam/pull/1310) ([tverbeiren](https://github.com/tverbeiren)) 
+- Remove back reference between VariantAnnotation and Variant [\#1297](https://github.com/bigdatagenomics/adam/pull/1297) ([fnothaft](https://github.com/fnothaft))
+- Reference region cleanup [\#1291](https://github.com/bigdatagenomics/adam/pull/1291) ([fnothaft](https://github.com/fnothaft))
+- Add docs about using ADAM's Kryo registrator from another Kryo registrator. [\#1305](https://github.com/bigdatagenomics/adam/pull/1305) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1224] Replace BroadcastRegionJoin with tree based algo. [\#1234](https://github.com/bigdatagenomics/adam/pull/1234) ([fnothaft](https://github.com/fnothaft))
+- Code style fixes [\#1299](https://github.com/bigdatagenomics/adam/pull/1299) ([heuermh](https://github.com/heuermh))
+- Make ADAMContext and JavaADAMContext constructors public [\#1298](https://github.com/bigdatagenomics/adam/pull/1298) ([heuermh](https://github.com/heuermh))
+- Add docs about building downstream applications [\#1304](https://github.com/bigdatagenomics/adam/pull/1304) ([heuermh](https://github.com/heuermh))
+- Misc shuffle join fixes. [\#1253](https://github.com/bigdatagenomics/adam/pull/1253) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-493] Add ADAM-on-Spark-on-YARN docs. [\#1301](https://github.com/bigdatagenomics/adam/pull/1301) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1280] Silence CRAM logging in tests. [\#1294](https://github.com/bigdatagenomics/adam/pull/1294) ([fnothaft](https://github.com/fnothaft))
+- add function:filterByOverlappingRegions [\#1287](https://github.com/bigdatagenomics/adam/pull/1287) ([liamlee](https://github.com/liamlee)) 
+- use ParsedLoci in loadIndexedBam [\#1277](https://github.com/bigdatagenomics/adam/pull/1277) ([ryan-williams](https://github.com/ryan-williams))
+- Increasing unit test coverage for VariantContextConverter [\#1276](https://github.com/bigdatagenomics/adam/pull/1276) ([heuermh](https://github.com/heuermh))
+- [ADAM-1233] Expose header lines in Variant-related GenomicRDDs [\#1260](https://github.com/bigdatagenomics/adam/pull/1260) ([fnothaft](https://github.com/fnothaft))
+- CGCloud deploy docs [\#1279](https://github.com/bigdatagenomics/adam/pull/1279) ([jpdna](https://github.com/jpdna))
+- Add VCF headers for fields in Variant and VariantAnnotation records [\#1281](https://github.com/bigdatagenomics/adam/pull/1281) ([heuermh](https://github.com/heuermh))
+- Expose FeatureRDD to public [\#1275](https://github.com/bigdatagenomics/adam/pull/1275) ([Georgehe4](https://github.com/Georgehe4)) 
+- Add docs for transform pipeline, ADAM-on-Toil [\#1262](https://github.com/bigdatagenomics/adam/pull/1262) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1083] Cleaning up `org.bdgenomics.adam.models`. [\#1267](https://github.com/bigdatagenomics/adam/pull/1267) ([fnothaft](https://github.com/fnothaft))
+- Clean up `org.bdgenomics.adam.rich` package. [\#1263](https://github.com/bigdatagenomics/adam/pull/1263) ([fnothaft](https://github.com/fnothaft))
+- Rename org.bdgenomics.adam.rdd.variation package to o.b.a.rdd.variant [\#1270](https://github.com/bigdatagenomics/adam/pull/1270) ([heuermh](https://github.com/heuermh))
+- Finishing up the cleanup on org.bdgenomics.adam.rdd. [\#1264](https://github.com/bigdatagenomics/adam/pull/1264) ([fnothaft](https://github.com/fnothaft))
+- use testFile in some tests [\#1268](https://github.com/bigdatagenomics/adam/pull/1268) ([ryan-williams](https://github.com/ryan-williams))
+- Upgrade to bdg-formats-0.10.0 [\#1135](https://github.com/bigdatagenomics/adam/pull/1135) ([fnothaft](https://github.com/fnothaft))
+- Merge VariantAnnotation and DatabaseVariantAnnotation records [\#1250](https://github.com/bigdatagenomics/adam/pull/1250) ([heuermh](https://github.com/heuermh))
+- make py file py3-forward-compatible [\#1266](https://github.com/bigdatagenomics/adam/pull/1266) ([ryan-williams](https://github.com/ryan-williams))
+- rm accidentally-added file [\#1265](https://github.com/bigdatagenomics/adam/pull/1265) ([fnothaft](https://github.com/fnothaft))
+- updates for bdg utils 0.2.9-SNAPSHOT [\#1261](https://github.com/bigdatagenomics/adam/pull/1261) ([akmorrow13](https://github.com/akmorrow13))
+- [ADAM-1225] Move helper functions from ADAMFunSuite to SparkFunSuite. [\#1251](https://github.com/bigdatagenomics/adam/pull/1251) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1196] Add support for open ReferenceRegions. [\#1252](https://github.com/bigdatagenomics/adam/pull/1252) ([fnothaft](https://github.com/fnothaft))
+- Rename org.bdgenomics.adam.rdd.features package to o.b.a.rdd.feature [\#1256](https://github.com/bigdatagenomics/adam/pull/1256) ([heuermh](https://github.com/heuermh))
+- [ADAM-1221] Bump Spark/Hadoop versions. [\#1258](https://github.com/bigdatagenomics/adam/pull/1258) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1221] Bump Spark/Hadoop versions. [\#1254](https://github.com/bigdatagenomics/adam/pull/1254) ([fnothaft](https://github.com/fnothaft))
+- Clean up documentation in `org.bdgenomics.adam.projection`. [\#1255](https://github.com/bigdatagenomics/adam/pull/1255) ([fnothaft](https://github.com/fnothaft))
+- Merge VariantAnnotation and DatabaseVariantAnnotation records [\#1144](https://github.com/bigdatagenomics/adam/pull/1144) ([heuermh](https://github.com/heuermh))
+- demonstrate multi-allelic gVCF failure - test added [\#1205](https://github.com/bigdatagenomics/adam/pull/1205) ([jpdna](https://github.com/jpdna))
+- Miscellaneous VCF fixes [\#1247](https://github.com/bigdatagenomics/adam/pull/1247) ([fnothaft](https://github.com/fnothaft))
+- [ADAM-1242] Clean up dead code in org.bdgenomics.adam.util. [\#1243](https://github.com/bigdatagenomics/adam/pull/1243) ([fnothaft](https://github.com/fnothaft))
+- Fix reads2coverage issues [\#1230](https://github.com/bigdatagenomics/adam/pull/1230) ([fnothaft](https://github.com/fnothaft))
+- Small cleanup of "replacing uses of deprecated class SAMFileReader" [\#1236](https://github.com/bigdatagenomics/adam/pull/1236) ([fnothaft](https://github.com/fnothaft))
+- replacing uses of deprecated class SAMFileReader [\#1235](https://github.com/bigdatagenomics/adam/pull/1235) ([lbergelson](https://github.com/lbergelson))
+- [ADAM-1212] Add empty assembly object, allows Maven build to create sources and javadoc artifacts [\#1215](https://github.com/bigdatagenomics/adam/pull/1215) ([heuermh](https://github.com/heuermh))
+- [ADAM-1211] Fix call to move_to_scala_2.sh, reorder Spark 2.x Scala 2.10 and 2.10 sections [\#1214](https://github.com/bigdatagenomics/adam/pull/1214) ([heuermh](https://github.com/heuermh))
+
 ### Version 0.20.0 ###
 
 **Closed issues:**