Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Sort pull requests by id #1345

Merged
merged 1 commit into from
Jan 8, 2017
Merged

Sort pull requests by id #1345

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
64 changes: 32 additions & 32 deletions CHANGES.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,68 +69,68 @@
**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-1334] Clean up serialization issues in Broadcast region join. [\#1336](https://github.com/bigdatagenomics/adam/pull/1336) ([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))
- [ADAM-1322] Skip git commit plugin if .git is missing. [\#1323](https://github.com/bigdatagenomics/adam/pull/1323) ([fnothaft](https://github.com/fnothaft))
- 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))
- Add interlocks for move_to_xyz scripts. [\#1319](https://github.com/bigdatagenomics/adam/pull/1319) ([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))
- [ADAM-1308] Fix stack overflow in join with custom iterator impl. [\#1315](https://github.com/bigdatagenomics/adam/pull/1315) ([fnothaft](https://github.com/fnothaft))
- 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))
- 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))
- Remove back reference between VariantAnnotation and Variant [\#1297](https://github.com/bigdatagenomics/adam/pull/1297) ([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))
- HBase as a separate repo [\#1293](https://github.com/bigdatagenomics/adam/pull/1293) ([jpdna](https://github.com/jpdna))
- Reference region cleanup [\#1291](https://github.com/bigdatagenomics/adam/pull/1291) ([fnothaft](https://github.com/fnothaft))
- Clean rewrite of VariantContextConverter [\#1288](https://github.com/bigdatagenomics/adam/pull/1288) ([fnothaft](https://github.com/fnothaft))
- add function:filterByOverlappingRegions [\#1287](https://github.com/bigdatagenomics/adam/pull/1287) ([liamlee](https://github.com/liamlee))
- Populate fields on VariantAnnotation [\#1283](https://github.com/bigdatagenomics/adam/pull/1283) ([heuermh](https://github.com/heuermh))
- Add VCF headers for fields in Variant and VariantAnnotation records [\#1281](https://github.com/bigdatagenomics/adam/pull/1281) ([heuermh](https://github.com/heuermh))
- CGCloud deploy docs [\#1279](https://github.com/bigdatagenomics/adam/pull/1279) ([jpdna](https://github.com/jpdna))
- some style nits [\#1278](https://github.com/bigdatagenomics/adam/pull/1278) ([ryan-williams](https://github.com/ryan-williams))
- 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))
- 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))
- 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))
- [ADAM-1083] Cleaning up `org.bdgenomics.adam.models`. [\#1267](https://github.com/bigdatagenomics/adam/pull/1267) ([fnothaft](https://github.com/fnothaft))
- 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))
- Finishing up the cleanup on org.bdgenomics.adam.rdd. [\#1264](https://github.com/bigdatagenomics/adam/pull/1264) ([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))
- Add docs for transform pipeline, ADAM-on-Toil [\#1262](https://github.com/bigdatagenomics/adam/pull/1262) ([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-1233] Expose header lines in Variant-related GenomicRDDs [\#1260](https://github.com/bigdatagenomics/adam/pull/1260) ([fnothaft](https://github.com/fnothaft))
- [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))
- 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))
- 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))
- [ADAM-1221] Bump Spark/Hadoop versions. [\#1254](https://github.com/bigdatagenomics/adam/pull/1254) ([fnothaft](https://github.com/fnothaft))
- Misc shuffle join fixes. [\#1253](https://github.com/bigdatagenomics/adam/pull/1253) ([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))
- [ADAM-1225] Move helper functions from ADAMFunSuite to SparkFunSuite. [\#1251](https://github.com/bigdatagenomics/adam/pull/1251) ([fnothaft](https://github.com/fnothaft))
- Merge VariantAnnotation and DatabaseVariantAnnotation records [\#1250](https://github.com/bigdatagenomics/adam/pull/1250) ([heuermh](https://github.com/heuermh))
- Miscellaneous VCF fixes [\#1247](https://github.com/bigdatagenomics/adam/pull/1247) ([fnothaft](https://github.com/fnothaft))
- HBase backend for Genotypes [\#1246](https://github.com/bigdatagenomics/adam/pull/1246) ([jpdna](https://github.com/jpdna))
- [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-1224] Replace BroadcastRegionJoin with tree based algo. [\#1234](https://github.com/bigdatagenomics/adam/pull/1234) ([fnothaft](https://github.com/fnothaft))
- Fix reads2coverage issues [\#1230](https://github.com/bigdatagenomics/adam/pull/1230) ([fnothaft](https://github.com/fnothaft))
- [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))
- demonstrate multi-allelic gVCF failure - test added [\#1205](https://github.com/bigdatagenomics/adam/pull/1205) ([jpdna](https://github.com/jpdna))
- Merge VariantAnnotation and DatabaseVariantAnnotation records [\#1144](https://github.com/bigdatagenomics/adam/pull/1144) ([heuermh](https://github.com/heuermh))
- Upgrade to bdg-formats-0.10.0 [\#1135](https://github.com/bigdatagenomics/adam/pull/1135) ([fnothaft](https://github.com/fnothaft))

### Version 0.20.0 ###

Expand Down