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# ADAM Changelog #
### Version 0.31.0 ###
**Closed issues:**
- Add deprecated annotations for code to be removed to support Spark 3 [\#2254](https://github.com/bigdatagenomics/adam/issues/2254)
- Update bdg-utils dependency version to 0.2.16 [\#2252](https://github.com/bigdatagenomics/adam/issues/2252)
- Bump Apache Spark dependency version to 2.4.5 [\#2248](https://github.com/bigdatagenomics/adam/issues/2248)
- FastqRecordConvert incompatible with single tube long fragment read headers [\#2246](https://github.com/bigdatagenomics/adam/issues/2246)
- Bam files with no unmapped reads fails to sort [\#2242](https://github.com/bigdatagenomics/adam/issues/2242)
- Unit test failure when building from release tarball [\#2241](https://github.com/bigdatagenomics/adam/issues/2241)
- Adam without HDFS [\#2238](https://github.com/bigdatagenomics/adam/issues/2238)
- Jenkins build status icon link is broken [\#2228](https://github.com/bigdatagenomics/adam/issues/2228)
- Write block-gzipped (bgzf) feature formats [\#2191](https://github.com/bigdatagenomics/adam/issues/2191)
- adam-submit is not exiting until I hit ctrl+C [\#2040](https://github.com/bigdatagenomics/adam/issues/2040)
- WARN VariantContextConverter:924 - Ran into Array Out of Bounds when accessing indices 0,1,2 of genotype . [\#2024](https://github.com/bigdatagenomics/adam/issues/2024)
- Add doc for running on HPC with PBS [\#2002](https://github.com/bigdatagenomics/adam/issues/2002)
- loadFastq with paired gzipped FASTQ files fails via s3a URLs [\#1855](https://github.com/bigdatagenomics/adam/issues/1855)
- Where to put lift over function [\#1811](https://github.com/bigdatagenomics/adam/issues/1811)
- Add transform to fix chromosome prefixes to genomic RDDs and CLIs [\#1757](https://github.com/bigdatagenomics/adam/issues/1757)
- Support using Spark-BAM to load BAM files [\#1683](https://github.com/bigdatagenomics/adam/issues/1683)
- Handling Validation Stringency without repeated code [\#1572](https://github.com/bigdatagenomics/adam/issues/1572)
- New model PartitionMap for Array[Option[(ReferenceRegion, ReferenceRegion)]] [\#1558](https://github.com/bigdatagenomics/adam/issues/1558)
- Revisit double-negative command line options (e.g. -disable_fast_concat) [\#1503](https://github.com/bigdatagenomics/adam/issues/1503)
- Improve test coverage for SAMRecord<->AlignmentRecord [\#1284](https://github.com/bigdatagenomics/adam/issues/1284)
- Allow alphabets to canonicalize strings [\#797](https://github.com/bigdatagenomics/adam/issues/797)
- Update MdTag.getReference for CIGAR N [\#742](https://github.com/bigdatagenomics/adam/issues/742)
- Replace contig length maps with sequence dictionary [\#572](https://github.com/bigdatagenomics/adam/issues/572)
- Use tool like Scala Refactoring to enforce import guidelines [\#445](https://github.com/bigdatagenomics/adam/issues/445)
**Merged and closed pull requests:**
- [ADAM-2254] Add deprecated annotations for code to be removed to support Spark 3 [\#2256](https://github.com/bigdatagenomics/adam/pull/2256) ([heuermh](https://github.com/heuermh))
- [ADAM-2252] Update bdg-utils dependency version to 0.2.16 [\#2253](https://github.com/bigdatagenomics/adam/pull/2253) ([heuermh](https://github.com/heuermh))
- [ADAM-2248] Bump Apache Spark dependency version to 2.4.5 [\#2249](https://github.com/bigdatagenomics/adam/pull/2249) ([heuermh](https://github.com/heuermh))
- [ADAM-2241] Commit template substitution may not be available if building from tarball [\#2243](https://github.com/bigdatagenomics/adam/pull/2243) ([heuermh](https://github.com/heuermh))
- [ADAM-2228] Remove Jenkins build status badge [\#2240](https://github.com/bigdatagenomics/adam/pull/2240) ([heuermh](https://github.com/heuermh))
- remove 2.7 support checks [\#2222](https://github.com/bigdatagenomics/adam/pull/2222) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2023] Implemented Duplicate Marking algorithm in Spark SQL [\#2045](https://github.com/bigdatagenomics/adam/pull/2045) ([jonpdeaton](https://github.com/jonpdeaton))
- use readlink to properly source source dir [\#2036](https://github.com/bigdatagenomics/adam/pull/2036) ([mtdeguzis](https://github.com/mtdeguzis))
- Don't discard unmapped reads in indel realignment [\#2019](https://github.com/bigdatagenomics/adam/pull/2019) ([pauldwolfe](https://github.com/pauldwolfe))
- Refactor/mark buckets [\#2015](https://github.com/bigdatagenomics/adam/pull/2015) ([jondeaton](https://github.com/jondeaton))
- Adding a BamLoader class to have only 1 header parse for multiple ind… [\#1966](https://github.com/bigdatagenomics/adam/pull/1966) ([ffinfo](https://github.com/ffinfo))
- Added additional arguments to GenomicRDD.pipe() [\#1758](https://github.com/bigdatagenomics/adam/pull/1758) ([gunjanbaid](https://github.com/gunjanbaid))
- Migrate bdg-formats to new adam-formats module. [\#1689](https://github.com/bigdatagenomics/adam/pull/1689) ([heuermh](https://github.com/heuermh))
- [ADAM-1683] Pull in Spark-BAM as a secondary loading path. [\#1686](https://github.com/bigdatagenomics/adam/pull/1686) ([fnothaft](https://github.com/fnothaft))
- Add SortedGenomicRDD trait, refactor shuffle joins and pipe [\#1590](https://github.com/bigdatagenomics/adam/pull/1590) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1513] Strandedness for FeatureRDDs [\#1555](https://github.com/bigdatagenomics/adam/pull/1555) ([devin-petersohn](https://github.com/devin-petersohn))
### Version 0.30.0 ###
**Closed issues:**
- Github changes plugin used in release script does not use two-factor authentication [\#2235](https://github.com/bigdatagenomics/adam/issues/2235)
- Update bdg-formats dependency version to 0.15.0 [\#2233](https://github.com/bigdatagenomics/adam/issues/2233)
- 7 tests failing on HEAD [\#2231](https://github.com/bigdatagenomics/adam/issues/2231)
- BUILD FAILURE - Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:java [\#2227](https://github.com/bigdatagenomics/adam/issues/2227)
- GenomicDataset saveAsParquet incorrectly named parameter compressCodec [\#2224](https://github.com/bigdatagenomics/adam/issues/2224)
- Add printAttributes methods for Reads, Sequences, Slices [\#2219](https://github.com/bigdatagenomics/adam/issues/2219)
- Add default Set.empty to printAttributes key method parameter [\#2218](https://github.com/bigdatagenomics/adam/issues/2218)
- Add Avro-friendly ctrs in rdd.variant package [\#2215](https://github.com/bigdatagenomics/adam/issues/2215)
- Cannot resolve adam-shade-spark2_2.11 dependency [\#2211](https://github.com/bigdatagenomics/adam/issues/2211)
**Merged and closed pull requests:**
- [ADAM-2235] Update github-changes-maven-plugin dependency version to 1.1 [\#2236](https://github.com/bigdatagenomics/adam/pull/2236) ([heuermh](https://github.com/heuermh))
- [ADAM-2233] Update bdg-formats dependency version to 0.15.0. [\#2234](https://github.com/bigdatagenomics/adam/pull/2234) ([heuermh](https://github.com/heuermh))
- Update maven plugin dependency versions. [\#2230](https://github.com/bigdatagenomics/adam/pull/2230) ([heuermh](https://github.com/heuermh))
- [ADAM-2224] Complete refactoring of compressionCodec for named parameter. [\#2229](https://github.com/bigdatagenomics/adam/pull/2229) ([heuermh](https://github.com/heuermh))
- [ADAM-2224] Use compressionCodec for named parameter. [\#2226](https://github.com/bigdatagenomics/adam/pull/2226) ([heuermh](https://github.com/heuermh))
- [ADAM-2219] Add printAttributes methods for Reads, Sequences, Slices [\#2223](https://github.com/bigdatagenomics/adam/pull/2223) ([heuermh](https://github.com/heuermh))
- [ADAM-2218] Add default Set.empty to printAttributes key method parameter. [\#2220](https://github.com/bigdatagenomics/adam/pull/2220) ([heuermh](https://github.com/heuermh))
- Rename AlignmentRecord to Alignment. [\#2217](https://github.com/bigdatagenomics/adam/pull/2217) ([heuermh](https://github.com/heuermh))
- [ADAM-2215] Add Avro-friendly ctrs to rdd.variant package [\#2216](https://github.com/bigdatagenomics/adam/pull/2216) ([heuermh](https://github.com/heuermh))
### Version 0.29.0 ###
**Closed issues:**
- Bump bdg-formats dependency version to 0.14.0 [\#2208](https://github.com/bigdatagenomics/adam/issues/2208)
- Bump Apache Spark dependency version to 2.4.4 [\#2202](https://github.com/bigdatagenomics/adam/issues/2202)
- Add missing loadVariantContexts(String, ValidationStringency) method [\#2197](https://github.com/bigdatagenomics/adam/issues/2197)
- Jenkins builds failing due to Coveralls API submission [\#2194](https://github.com/bigdatagenomics/adam/issues/2194)
- Confirm block-gzipped (bgzf) interleaved FASTQ is supported [\#2193](https://github.com/bigdatagenomics/adam/issues/2193)
- TransformGenotype/Variant do not support compressed VCF [\#2190](https://github.com/bigdatagenomics/adam/issues/2190)
- Add htsjdk conversion methods to VariantContextDataset [\#2189](https://github.com/bigdatagenomics/adam/issues/2189)
- TransformVariants is missing partition arguments [\#2188](https://github.com/bigdatagenomics/adam/issues/2188)
- StackOverflowError when saving to BAM in adam-shell [\#2186](https://github.com/bigdatagenomics/adam/issues/2186)
- loadFastaDna usage not obvious due to default method parameter [\#2183](https://github.com/bigdatagenomics/adam/issues/2183)
- loadFastaDna does not seem to work [\#2182](https://github.com/bigdatagenomics/adam/issues/2182)
- kryo buffer overflow when converting fastas from CLI to adam [\#1660](https://github.com/bigdatagenomics/adam/issues/1660)
**Merged and closed pull requests:**
- [ADAM-2208] Bump bdg-formats dependency version to 0.14.0 [\#2209](https://github.com/bigdatagenomics/adam/pull/2209) ([heuermh](https://github.com/heuermh))
- Add FASTA in formatter for sequence datasets [\#2207](https://github.com/bigdatagenomics/adam/pull/2207) ([heuermh](https://github.com/heuermh))
- Remove Avro 1.8.x download step from Jenkins Scala 2.12 installation. [\#2206](https://github.com/bigdatagenomics/adam/pull/2206) ([heuermh](https://github.com/heuermh))
- Use qualityScores for base quality scores [\#2205](https://github.com/bigdatagenomics/adam/pull/2205) ([heuermh](https://github.com/heuermh))
- [ADAM-2189] Add htsjdk conversion methods to VariantContextDataset [\#2204](https://github.com/bigdatagenomics/adam/pull/2204) ([heuermh](https://github.com/heuermh))
- [ADAM-2202] Bump Apache Spark dependency version to 2.4.4. [\#2203](https://github.com/bigdatagenomics/adam/pull/2203) ([heuermh](https://github.com/heuermh))
- [ADAM-2183] Drop default value for maximumLength [\#2201](https://github.com/bigdatagenomics/adam/pull/2201) ([heuermh](https://github.com/heuermh))
- [ADAM-2197] Add missing loadVariantContexts(String, ValidationStringency) method [\#2200](https://github.com/bigdatagenomics/adam/pull/2200) ([heuermh](https://github.com/heuermh))
- [ADAM-2194] Disable coveralls reporting from Jenkins test script [\#2196](https://github.com/bigdatagenomics/adam/pull/2196) ([heuermh](https://github.com/heuermh))
- [ADAM-2188] Add partition cli args to TransformVariants,Features. [\#2192](https://github.com/bigdatagenomics/adam/pull/2192) ([heuermh](https://github.com/heuermh))
- Bump htsjdk dependency version to 2.19.0 [\#2184](https://github.com/bigdatagenomics/adam/pull/2184) ([heuermh](https://github.com/heuermh))
- Update required Maven version in docs [\#2181](https://github.com/bigdatagenomics/adam/pull/2181) ([heuermh](https://github.com/heuermh))
### Version 0.28.0 ###
**Closed issues:**
- Bump bdg-formats dependency version to 0.13.0 [\#2177](https://github.com/bigdatagenomics/adam/issues/2177)
- Rename reads to alignments in methods where appropriate [\#2172](https://github.com/bigdatagenomics/adam/issues/2172)
- Add command line option re: creating references from FASTA sources [\#2168](https://github.com/bigdatagenomics/adam/issues/2168)
- Add command line support for loading references in TransformFeatures [\#2167](https://github.com/bigdatagenomics/adam/issues/2167)
- Add load methods for data frames [\#2159](https://github.com/bigdatagenomics/adam/issues/2159)
- Transform VCF to adam file not found exception. [\#2076](https://github.com/bigdatagenomics/adam/issues/2076)
- NoClassDefFoundError: javax/tools/ToolProvider on openjdk 10.0.2 [\#2030](https://github.com/bigdatagenomics/adam/issues/2030)
- NotSerializableException: com.netflix.servo.monitor.LongGauge [\#1952](https://github.com/bigdatagenomics/adam/issues/1952)
- Should NucleotideContigFragmentRDD create sequence dictionary on load? [\#1894](https://github.com/bigdatagenomics/adam/issues/1894)
- converting fasta to adam eats a huge ammount of time and memory [\#1891](https://github.com/bigdatagenomics/adam/issues/1891)
- Support minPartitions parameter across load calls [\#1792](https://github.com/bigdatagenomics/adam/issues/1792)
- make reading fasta less memory hungry [\#1458](https://github.com/bigdatagenomics/adam/issues/1458)
- Improve unit test coverage for NucleotideContigFragmentRDD [\#1413](https://github.com/bigdatagenomics/adam/issues/1413)
- Support for INSDC Sequence records (i.e., Genbank/EMBL format)? [\#1219](https://github.com/bigdatagenomics/adam/issues/1219)
**Merged and closed pull requests:**
- [ADAM-2177] Bump bdg-formats dependency version to 0.13.0 [\#2178](https://github.com/bigdatagenomics/adam/pull/2178) ([heuermh](https://github.com/heuermh))
- [ADAM-2172] Rename reads to alignments in methods where appropriate [\#2176](https://github.com/bigdatagenomics/adam/pull/2176) ([heuermh](https://github.com/heuermh))
- [ADAM-1891] Reimplement FASTA sequence and slice converters for performance [\#2175](https://github.com/bigdatagenomics/adam/pull/2175) ([heuermh](https://github.com/heuermh))
- [ADAM-2168] Add command line option re: creating references from FASTA sources [\#2170](https://github.com/bigdatagenomics/adam/pull/2170) ([heuermh](https://github.com/heuermh))
- [ADAM-2167] Add command line support for loading references in TransformFeatures [\#2169](https://github.com/bigdatagenomics/adam/pull/2169) ([heuermh](https://github.com/heuermh))
- bump adam-python version [\#2165](https://github.com/bigdatagenomics/adam/pull/2165) ([akmorrow13](https://github.com/akmorrow13))
- Convert fragment dataset to alignment dataset directly [\#2162](https://github.com/bigdatagenomics/adam/pull/2162) ([heuermh](https://github.com/heuermh))
- [ADAM-2159] Add load methods for data frames [\#2158](https://github.com/bigdatagenomics/adam/pull/2158) ([heuermh](https://github.com/heuermh))
- Post 0.27.0 release cleanup and doc fixes. [\#2155](https://github.com/bigdatagenomics/adam/pull/2155) ([heuermh](https://github.com/heuermh))
- Add direct conversion from DatasetBoundFragmentRDD to DatasetBoundAli… [\#2016](https://github.com/bigdatagenomics/adam/pull/2016) ([henrydavidge](https://github.com/henrydavidge))
- Add ADAMContext APIs to create genomic RDDs from dataframes [\#2000](https://github.com/bigdatagenomics/adam/pull/2000) ([henrydavidge](https://github.com/henrydavidge))
- Adding ReadRDD, SequenceRDD, and SliceRDD. [\#1895](https://github.com/bigdatagenomics/adam/pull/1895) ([heuermh](https://github.com/heuermh))
### Version 0.27.0 ###
**Closed issues:**
- Add Scala 2.12 artifacts to release script [\#2153](https://github.com/bigdatagenomics/adam/issues/2153)
- Tried to access method org.apache.avro.specific.SpecificData.<init>()V from class ProcessingStep [\#2151](https://github.com/bigdatagenomics/adam/issues/2151)
- Update maven-jar-plugin dependency version to 3.1.2 [\#2147](https://github.com/bigdatagenomics/adam/issues/2147)
- Homebrew and Bioconda packages fail against Spark 2.4.2 [\#2146](https://github.com/bigdatagenomics/adam/issues/2146)
- Add Spark 2.4.3 and Scala 2.12 to Jenkins build [\#2145](https://github.com/bigdatagenomics/adam/issues/2145)
- Can encounter empty reduce when BAM header fails validation [\#2143](https://github.com/bigdatagenomics/adam/issues/2143)
- Build failing in jenkins from Spark 2.2.3 [\#2139](https://github.com/bigdatagenomics/adam/issues/2139)
- Make SamRecordConverter public [\#2138](https://github.com/bigdatagenomics/adam/issues/2138)
- python API does not match API [\#2127](https://github.com/bigdatagenomics/adam/issues/2127)
- Error when run : mvn install [\#2123](https://github.com/bigdatagenomics/adam/issues/2123)
- Always use Spark SQL in GenomicDataset read path [\#2114](https://github.com/bigdatagenomics/adam/issues/2114)
- Update bdg-utils dependency version to 0.2.14 [\#2106](https://github.com/bigdatagenomics/adam/issues/2106)
- NoSuchMethodError: org.apache.parquet.column.ParquetProperties.getAllocator()Lorg/apache/parquet/bytes/ByteBufferAllocator [\#2098](https://github.com/bigdatagenomics/adam/issues/2098)
- ClassNotFoundException: org.apache.avro.message.BinaryMessageEncoder [\#2091](https://github.com/bigdatagenomics/adam/issues/2091)
- Release script needs to touch Version in R DESCRIPTION file [\#2089](https://github.com/bigdatagenomics/adam/issues/2089)
- org.apache.avro.SchemaParseException: Can't redefine: list [\#2058](https://github.com/bigdatagenomics/adam/issues/2058)
- Support Spark 2.4 and Scala 2.12 [\#2044](https://github.com/bigdatagenomics/adam/issues/2044)
- Fail early when output directory already exists [\#2034](https://github.com/bigdatagenomics/adam/issues/2034)
- NoClassDefFoundError o.a.parquet.hadoop.metadata.CompressionCodecName [\#1742](https://github.com/bigdatagenomics/adam/issues/1742)
- Log with parameterized messages consistently for performance [\#1712](https://github.com/bigdatagenomics/adam/issues/1712)
**Merged and closed pull requests:**
- [ADAM-2153] Add Scala 2.12 artifacts to release script [\#2154](https://github.com/bigdatagenomics/adam/pull/2154) ([heuermh](https://github.com/heuermh))
- [ADAM-2089] Bump Version in R DESCRIPTION file [\#2152](https://github.com/bigdatagenomics/adam/pull/2152) ([heuermh](https://github.com/heuermh))
- [ADAM-2145] Add Spark 2.4.3 and Scala 2.12 to Jenkins build [\#2149](https://github.com/bigdatagenomics/adam/pull/2149) ([heuermh](https://github.com/heuermh))
- [ADAM-2147] Update maven-jar-plugin dependency version to 3.1.2. [\#2148](https://github.com/bigdatagenomics/adam/pull/2148) ([heuermh](https://github.com/heuermh))
- [ADAM-2143] Use fold instead of reduce when loading SAM/BAM/CRAM headers [\#2144](https://github.com/bigdatagenomics/adam/pull/2144) ([fnothaft](https://github.com/fnothaft))
- Remove parquet-scala dependency from dependencyManagement. [\#2142](https://github.com/bigdatagenomics/adam/pull/2142) ([heuermh](https://github.com/heuermh))
- [ADAM-2139] Update Spark version to 2.3.3 for Jenkins test [\#2141](https://github.com/bigdatagenomics/adam/pull/2141) ([heuermh](https://github.com/heuermh))
- [ADAM-1712] Replace utils.Logger with grizzled.slf4j.Logger [\#2136](https://github.com/bigdatagenomics/adam/pull/2136) ([heuermh](https://github.com/heuermh))
- [ADAM-2034] Check output path is writeable before running transformations [\#2135](https://github.com/bigdatagenomics/adam/pull/2135) ([heuermh](https://github.com/heuermh))
- jenkins scripts deletes conda envs [\#2133](https://github.com/bigdatagenomics/adam/pull/2133) ([akmorrow13](https://github.com/akmorrow13))
- Update htsjdk dependency version to 2.18.2 [\#2132](https://github.com/bigdatagenomics/adam/pull/2132) ([heuermh](https://github.com/heuermh))
- [ADAM-2127] Update python doc per GenomicRdd --> GenomicDataset change [\#2128](https://github.com/bigdatagenomics/adam/pull/2128) ([heuermh](https://github.com/heuermh))
- Update python and R versions. [\#2126](https://github.com/bigdatagenomics/adam/pull/2126) ([heuermh](https://github.com/heuermh))
- use parquet-scala_2.11 fork [\#2108](https://github.com/bigdatagenomics/adam/pull/2108) ([ryan-williams](https://github.com/ryan-williams))
- [ADAM-2106] Update bdg-utils dependency version to 0.2.14 [\#2107](https://github.com/bigdatagenomics/adam/pull/2107) ([heuermh](https://github.com/heuermh))
- [ADAM-2044] Update Spark version to 2.4.3, add move to Scala 2.12 script [\#2056](https://github.com/bigdatagenomics/adam/pull/2056) ([heuermh](https://github.com/heuermh))
### Version 0.26.0 ###
**Closed issues:**
- Bump Spark dependency to version 2.3.3 [\#2120](https://github.com/bigdatagenomics/adam/issues/2120)
- Update Spark version on Jenkins to 2.2.3 [\#2115](https://github.com/bigdatagenomics/adam/issues/2115)
- Inverted duplicates are not found in mark duplicates [\#2102](https://github.com/bigdatagenomics/adam/issues/2102)
- Py4JError: org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator.fromKnowns does not exist in the JVM [\#2099](https://github.com/bigdatagenomics/adam/issues/2099)
- Update Bioconda recipe for ADAM 0.25.0 [\#2088](https://github.com/bigdatagenomics/adam/issues/2088)
- Update Homebrew formula for ADAM 0.25.0 [\#2087](https://github.com/bigdatagenomics/adam/issues/2087)
- Error: Dependency package(s) 'SparkR' not available [\#2086](https://github.com/bigdatagenomics/adam/issues/2086)
- Java-friendly indel realignment method doesn't allow passing reference [\#2013](https://github.com/bigdatagenomics/adam/issues/2013)
- Use consistent (Scala-specific) (Java-specific) qualifiers in method scaladoc [\#1986](https://github.com/bigdatagenomics/adam/issues/1986)
- Clarify GenomicRDD vs. GenomicDataset name [\#1954](https://github.com/bigdatagenomics/adam/issues/1954)
- Support validation stringency in out formatters [\#1949](https://github.com/bigdatagenomics/adam/issues/1949)
- Compute coverage by sample [\#1498](https://github.com/bigdatagenomics/adam/issues/1498)
**Merged and closed pull requests:**
- Bump bdg-formats dependency to version 0.12.0. [\#2124](https://github.com/bigdatagenomics/adam/pull/2124) ([heuermh](https://github.com/heuermh))
- [ADAM-2120] Bump Spark dependency to version 2.3.3. [\#2121](https://github.com/bigdatagenomics/adam/pull/2121) ([heuermh](https://github.com/heuermh))
- Filter supplemental reads from scoring [\#2119](https://github.com/bigdatagenomics/adam/pull/2119) ([pauldwolfe](https://github.com/pauldwolfe))
- [ADAM-2115] Update Spark version on Jenkins to 2.2.3. [\#2118](https://github.com/bigdatagenomics/adam/pull/2118) ([heuermh](https://github.com/heuermh))
- Refactor AlignmentRecord, RecordGroup, and ProcessingStep [\#2113](https://github.com/bigdatagenomics/adam/pull/2113) ([heuermh](https://github.com/heuermh))
- removed anaconda requirement for venv during jenkins test [\#2109](https://github.com/bigdatagenomics/adam/pull/2109) ([akmorrow13](https://github.com/akmorrow13))
- Propagate read negative flag to SAM records for unmapped reads [\#2105](https://github.com/bigdatagenomics/adam/pull/2105) ([henrydavidge](https://github.com/henrydavidge))
- Add consensus targets to realignment targets [\#2104](https://github.com/bigdatagenomics/adam/pull/2104) ([pauldwolfe](https://github.com/pauldwolfe))
- [ADAM-2099] Add python realignIndelsFromKnownIndels method [\#2103](https://github.com/bigdatagenomics/adam/pull/2103) ([heuermh](https://github.com/heuermh))
- [ADAM-2102] Inverted duplicates are not found in mark duplicates [\#2101](https://github.com/bigdatagenomics/adam/pull/2101) ([pauldwolfe](https://github.com/pauldwolfe))
- Rename contig to reference [\#2100](https://github.com/bigdatagenomics/adam/pull/2100) ([heuermh](https://github.com/heuermh))
- [ADAM-1986] Add java-specific methods where missing. [\#2097](https://github.com/bigdatagenomics/adam/pull/2097) ([heuermh](https://github.com/heuermh))
- [ADAM-2013] Add java-friendly indel realignment method that accepts reference. [\#2095](https://github.com/bigdatagenomics/adam/pull/2095) ([heuermh](https://github.com/heuermh))
- Use build-helper-maven-plugin for build timestamp [\#2093](https://github.com/bigdatagenomics/adam/pull/2093) ([heuermh](https://github.com/heuermh))
- bump adam-python version to 0.25.0a0 [\#2092](https://github.com/bigdatagenomics/adam/pull/2092) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2085] Update R installation docs re: libgit2 and SparkR. [\#2090](https://github.com/bigdatagenomics/adam/pull/2090) ([heuermh](https://github.com/heuermh))
- [ADAM-1954] Complete refactoring GenomicRDD to GenomicDataset. [\#1981](https://github.com/bigdatagenomics/adam/pull/1981) ([heuermh](https://github.com/heuermh))
- [ADAM-1949] Support validation stringency in out formatters. [\#1969](https://github.com/bigdatagenomics/adam/pull/1969) ([heuermh](https://github.com/heuermh))
### Version 0.25.0 ###
**Closed issues:**
- Expand illumina metadata regex to include "N" character [\#2079](https://github.com/bigdatagenomics/adam/issues/2079)
- Remove support for Hadoop 2.6 [\#2073](https://github.com/bigdatagenomics/adam/issues/2073)
- NumberFormatException: For input string: "nan" in VCF [\#2068](https://github.com/bigdatagenomics/adam/issues/2068)
- Support Spark 2.3.2 [\#2062](https://github.com/bigdatagenomics/adam/issues/2062)
- Arrays should be passed to HTSJDK in the JVM primitive type [\#2059](https://github.com/bigdatagenomics/adam/issues/2059)
- toCoverage() function for alignments does not distinguish samples [\#2049](https://github.com/bigdatagenomics/adam/issues/2049)
- Building from adam-core module directory fails to generate Scala code for sql package [\#2047](https://github.com/bigdatagenomics/adam/issues/2047)
- Data Sets [\#2043](https://github.com/bigdatagenomics/adam/issues/2043)
- saveAsBed writes missing score values as '.' instead of '0' [\#2039](https://github.com/bigdatagenomics/adam/issues/2039)
- Fix GFF3 parser to handle trailing FASTA [\#2037](https://github.com/bigdatagenomics/adam/issues/2037)
- Add StorageLevel as an optional parameter to loadPairedFastq [\#2032](https://github.com/bigdatagenomics/adam/issues/2032)
- Error: File name too long when building on encrypted file system [\#2031](https://github.com/bigdatagenomics/adam/issues/2031)
- Fail to transform a VCF file containing multiple genome data (Muliple sample) [\#2029](https://github.com/bigdatagenomics/adam/issues/2029)
- Dataset and RDD constructors are missing from CoverageRDD [\#2027](https://github.com/bigdatagenomics/adam/issues/2027)
- How to create a single RDD[Genotype] object out of multiple VCF files? [\#2025](https://github.com/bigdatagenomics/adam/issues/2025)
- ReadTheDocs github banner is broken [\#2020](https://github.com/bigdatagenomics/adam/issues/2020)
- -realign_indels throws serialization error with instrumentation enabled [\#2007](https://github.com/bigdatagenomics/adam/issues/2007)
- Support 0 length FASTQ reads [\#2006](https://github.com/bigdatagenomics/adam/issues/2006)
- Speed of Reading into ADAM RDDs from S3 [\#2003](https://github.com/bigdatagenomics/adam/issues/2003)
- Support Python 3 [\#1999](https://github.com/bigdatagenomics/adam/issues/1999)
- Unordered list of region join types in doc is missing nested levels [\#1997](https://github.com/bigdatagenomics/adam/issues/1997)
- Add VariantContextRDD.saveAsPartitionedParquet, ADAMContext.loadPartitionedParquetVariantContexts [\#1996](https://github.com/bigdatagenomics/adam/issues/1996)
- VCF annotation question [\#1994](https://github.com/bigdatagenomics/adam/issues/1994)
- Fastq reader clips long reads at 10,000 bp [\#1992](https://github.com/bigdatagenomics/adam/issues/1992)
- adam-submit Error: Number of executors must be a positive number on EMR 5.13.0/Spark 2.3.0 [\#1991](https://github.com/bigdatagenomics/adam/issues/1991)
- Test against Spark 2.3.1, Parquet 1.8.3 [\#1989](https://github.com/bigdatagenomics/adam/issues/1989)
- END does not get set when writing a gVCF [\#1988](https://github.com/bigdatagenomics/adam/issues/1988)
- Support saving single files to filesystems that don't implement getScheme [\#1984](https://github.com/bigdatagenomics/adam/issues/1984)
- Add additional filter by convenience methods [\#1978](https://github.com/bigdatagenomics/adam/issues/1978)
- Limiting FragmentRDD pipe paralellism [\#1977](https://github.com/bigdatagenomics/adam/issues/1977)
- Consider javadoc.io for API documentation linking [\#1976](https://github.com/bigdatagenomics/adam/issues/1976)
- FASTQ Reader leaks connections [\#1974](https://github.com/bigdatagenomics/adam/issues/1974)
- Update bioconda recipe for version 0.24.0 [\#1971](https://github.com/bigdatagenomics/adam/issues/1971)
- Update homebrew formula at brewsci/homebrew-bio for version 0.24.0 [\#1970](https://github.com/bigdatagenomics/adam/issues/1970)
- loadPartitionedParquetAlignments fails with Reference.all [\#1967](https://github.com/bigdatagenomics/adam/issues/1967)
- Caused by: java.lang.VerifyError: class com.fasterxml.jackson.module.scala.ser.ScalaIteratorSerializer overrides final method withResolved [\#1953](https://github.com/bigdatagenomics/adam/issues/1953)
- FASTQ input format needs to support index sequences [\#1697](https://github.com/bigdatagenomics/adam/issues/1697)
- Changelog must be edited and committed manually during release process [\#936](https://github.com/bigdatagenomics/adam/issues/936)
**Merged and closed pull requests:**
- added pyspark mock modules for API documentation [\#2084](https://github.com/bigdatagenomics/adam/pull/2084) ([akmorrow13](https://github.com/akmorrow13))
- Added mock python modules for API python documentation [\#2082](https://github.com/bigdatagenomics/adam/pull/2082) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2079] Expand illumina metadata regex to include "N" character [\#2081](https://github.com/bigdatagenomics/adam/pull/2081) ([pauldwolfe](https://github.com/pauldwolfe))
- ADAM-2079 Added "N" to regexs for illumina metadata [\#2080](https://github.com/bigdatagenomics/adam/pull/2080) ([pauldwolfe](https://github.com/pauldwolfe))
- Update docs with new template and documentation [\#2078](https://github.com/bigdatagenomics/adam/pull/2078) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1992] Make maximum FASTQ read length configurable. [\#2077](https://github.com/bigdatagenomics/adam/pull/2077) ([heuermh](https://github.com/heuermh))
- [ADAM-2059] Properly pass back primitive typed arrays to HTSJDK. [\#2075](https://github.com/bigdatagenomics/adam/pull/2075) ([heuermh](https://github.com/heuermh))
- Update dependency versions, including htsjdk to 2.16.1 and guava to 27.0-jre [\#2072](https://github.com/bigdatagenomics/adam/pull/2072) ([heuermh](https://github.com/heuermh))
- [ADAM-1999] Support Python 3 [\#2070](https://github.com/bigdatagenomics/adam/pull/2070) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2068] Prevent NumberFormatException for nan vs NaN in VCF files. [\#2069](https://github.com/bigdatagenomics/adam/pull/2069) ([heuermh](https://github.com/heuermh))
- Update python MAKE file [\#2067](https://github.com/bigdatagenomics/adam/pull/2067) ([Georgehe4](https://github.com/Georgehe4))
- Update python MAKE file [\#2066](https://github.com/bigdatagenomics/adam/pull/2066) ([Georgehe4](https://github.com/Georgehe4))
- Update jenkins script to test python 3.6 [\#2060](https://github.com/bigdatagenomics/adam/pull/2060) ([Georgehe4](https://github.com/Georgehe4))
- [ADAM-2062] Update Spark version to 2.3.2 [\#2055](https://github.com/bigdatagenomics/adam/pull/2055) ([heuermh](https://github.com/heuermh))
- Clean up fields and doc in fragment. [\#2054](https://github.com/bigdatagenomics/adam/pull/2054) ([heuermh](https://github.com/heuermh))
- [ADAM-2037] Support GFF3 files containing FASTA formatted sequences. [\#2053](https://github.com/bigdatagenomics/adam/pull/2053) ([heuermh](https://github.com/heuermh))
- modified CoverageRDD and FeatureRDD to extend MultisampleGenomicDataset [\#2051](https://github.com/bigdatagenomics/adam/pull/2051) ([akmorrow13](https://github.com/akmorrow13))
- Multi-sample coverage [\#2050](https://github.com/bigdatagenomics/adam/pull/2050) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2047] Use source directory relative to project.basedir for adam codegen. [\#2048](https://github.com/bigdatagenomics/adam/pull/2048) ([heuermh](https://github.com/heuermh))
- [ADAM-2039] Adding support for writing BED format per UCSC definition [\#2042](https://github.com/bigdatagenomics/adam/pull/2042) ([heuermh](https://github.com/heuermh))
- Update Jenkins Spark version to 2.2.2 [\#2035](https://github.com/bigdatagenomics/adam/pull/2035) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-2032] Add StorageLevel as an optional parameter to loadPairedFastq [\#2033](https://github.com/bigdatagenomics/adam/pull/2033) ([heuermh](https://github.com/heuermh))
- [ADAM-2027] Add RDD and Dataset constructors to CoverageRDD. [\#2028](https://github.com/bigdatagenomics/adam/pull/2028) ([heuermh](https://github.com/heuermh))
- Allow for export of query name sorted SAM files [\#2026](https://github.com/bigdatagenomics/adam/pull/2026) ([karenfeng](https://github.com/karenfeng))
- [ADAM-2020] Fix ReadTheDocs Github banner. [\#2021](https://github.com/bigdatagenomics/adam/pull/2021) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1988] Add copyVariantEndToAttribute method to support gVCF END attribute … [\#2017](https://github.com/bigdatagenomics/adam/pull/2017) ([heuermh](https://github.com/heuermh))
- [ADAM-936] Use github-changes-maven-plugin to update CHANGES.md. [\#2014](https://github.com/bigdatagenomics/adam/pull/2014) ([heuermh](https://github.com/heuermh))
- [ADAM-1992] Make maximum FASTQ read length configurable. [\#2011](https://github.com/bigdatagenomics/adam/pull/2011) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1697] Expand Illumina metadata regex to cover interleaved index sequences. [\#2010](https://github.com/bigdatagenomics/adam/pull/2010) ([heuermh](https://github.com/heuermh))
- [ADAM-2007] Make IndelRealignmentTarget implement Serializable. [\#2009](https://github.com/bigdatagenomics/adam/pull/2009) ([fnothaft](https://github.com/fnothaft))
- [ADAM-2006] Support loading 0-length reads as FASTQ. [\#2008](https://github.com/bigdatagenomics/adam/pull/2008) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1697] Expand Illumina metadata regex to cover index sequences [\#2004](https://github.com/bigdatagenomics/adam/pull/2004) ([pauldwolfe](https://github.com/pauldwolfe))
- [ADAM-1996] Load and save VariantContexts as partitioned Parquet. [\#2001](https://github.com/bigdatagenomics/adam/pull/2001) ([heuermh](https://github.com/heuermh))
- [ADAM-1997] Nest list of region join types in joins doc. [\#1998](https://github.com/bigdatagenomics/adam/pull/1998) ([heuermh](https://github.com/heuermh))
- [ADAM-1877] Add filterToReferenceName(s) to SequenceDictionary. [\#1995](https://github.com/bigdatagenomics/adam/pull/1995) ([heuermh](https://github.com/heuermh))
- [ADAM-1984] Support file systems that don't set the scheme. [\#1985](https://github.com/bigdatagenomics/adam/pull/1985) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1978] Add additional filter by convenience methods. [\#1983](https://github.com/bigdatagenomics/adam/pull/1983) ([heuermh](https://github.com/heuermh))
- Adding printAttribute methods for alignment records, features, and samples. [\#1982](https://github.com/bigdatagenomics/adam/pull/1982) ([heuermh](https://github.com/heuermh))
- Fix partitioning code to use Long instead of Int [\#1980](https://github.com/bigdatagenomics/adam/pull/1980) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1976] Adding core API documentation link and badge. [\#1979](https://github.com/bigdatagenomics/adam/pull/1979) ([heuermh](https://github.com/heuermh))
- [ADAM-1974] Close unclosed stream in FastqInputFormat. [\#1975](https://github.com/bigdatagenomics/adam/pull/1975) ([fnothaft](https://github.com/fnothaft))
- Set defaults to schemas [\#1972](https://github.com/bigdatagenomics/adam/pull/1972) ([ffinfo](https://github.com/ffinfo))
- Add loadPairedFastqAsFragments method. [\#1866](https://github.com/bigdatagenomics/adam/pull/1866) ([heuermh](https://github.com/heuermh))
- Adding loadPairedFastqAsFragments method [\#1828](https://github.com/bigdatagenomics/adam/pull/1828) ([ffinfo](https://github.com/ffinfo))
### Version 0.24.0 ###
**Closed issues:**
- Phred values from 156–254 do not round trip properly between log space [\#1964](https://github.com/bigdatagenomics/adam/issues/1964)
- Support VCF lines with positions at 0 [\#1959](https://github.com/bigdatagenomics/adam/issues/1959)
- Don't initialize non-ref values to Int.MinValue [\#1957](https://github.com/bigdatagenomics/adam/issues/1957)
- Support downsampling in recalibration [\#1955](https://github.com/bigdatagenomics/adam/issues/1955)
- Cannot waive validation stringency for INFO Number=.,Type=Flag fields [\#1939](https://github.com/bigdatagenomics/adam/issues/1939)
- Clip phred scores below Int.MaxValue [\#1934](https://github.com/bigdatagenomics/adam/issues/1934)
- ADAMContext.getFsAndFilesWithFilter should throw exception if paths null or empty [\#1932](https://github.com/bigdatagenomics/adam/issues/1932)
- Bump to Spark 2.3.0 [\#1931](https://github.com/bigdatagenomics/adam/issues/1931)
- util.FileExtensions should be public for use downstream in Cannoli [\#1927](https://github.com/bigdatagenomics/adam/issues/1927)
- Reduce logging level for ADAMKryoRegistrator [\#1925](https://github.com/bigdatagenomics/adam/issues/1925)
- Revisit performance implications of commit 1eed8e8 [\#1923](https://github.com/bigdatagenomics/adam/issues/1923)
- add akmorrow13 to PyPl for bdgenomics.adam [\#1919](https://github.com/bigdatagenomics/adam/issues/1919)
- Read the Docs build failing with TypeError: super() argument 1 must be type, not None [\#1917](https://github.com/bigdatagenomics/adam/issues/1917)
- Bump Hadoop-BAM dependency to 7.9.2. [\#1915](https://github.com/bigdatagenomics/adam/issues/1915)
- cannot run pyadam from adam distribution 0.23.0 [\#1914](https://github.com/bigdatagenomics/adam/issues/1914)
- adam2fasta/q are missing asSingleFile, disableFastConcat [\#1912](https://github.com/bigdatagenomics/adam/issues/1912)
- Pipe API doesn't properly handle multiple arguments and spaces [\#1909](https://github.com/bigdatagenomics/adam/issues/1909)
- Bump to HTSJDK 2.13.2 [\#1907](https://github.com/bigdatagenomics/adam/issues/1907)
- S3A error: HTTP request: Timeout waiting for connection from pool [\#1906](https://github.com/bigdatagenomics/adam/issues/1906)
- InputStream passed to VCFHeaderReader does not get closed [\#1900](https://github.com/bigdatagenomics/adam/issues/1900)
- Support INFO fields set to missing [\#1898](https://github.com/bigdatagenomics/adam/issues/1898)
- CLI to transfer between cloud storage and HDFS [\#1896](https://github.com/bigdatagenomics/adam/issues/1896)
- Jenkins does not run python or R tests [\#1889](https://github.com/bigdatagenomics/adam/issues/1889)
- pyadam throws application option error [\#1886](https://github.com/bigdatagenomics/adam/issues/1886)
- ReferenceRegion in python does not exist [\#1884](https://github.com/bigdatagenomics/adam/issues/1884)
- Caching GenomicRDD in pyspark [\#1883](https://github.com/bigdatagenomics/adam/issues/1883)
- adam-submit aborts if ADAM_HOME is set [\#1882](https://github.com/bigdatagenomics/adam/issues/1882)
- Allow piped commands to timeout [\#1875](https://github.com/bigdatagenomics/adam/issues/1875)
- loadVcf does not dedupe sample ID [\#1874](https://github.com/bigdatagenomics/adam/issues/1874)
- Add coverage command for reporting read coverage [\#1873](https://github.com/bigdatagenomics/adam/issues/1873)
- Only python 2? [\#1871](https://github.com/bigdatagenomics/adam/issues/1871)
- Support VariantContextRDD from SQL [\#1867](https://github.com/bigdatagenomics/adam/issues/1867)
- Cannot find `find-adam-assembly.sh` in bioconda build [\#1862](https://github.com/bigdatagenomics/adam/issues/1862)
- `_jvm.java.lang.Class.forName` does not work for certain configurations [\#1858](https://github.com/bigdatagenomics/adam/issues/1858)
- Formatting error in CHANGES.md [\#1857](https://github.com/bigdatagenomics/adam/issues/1857)
- Various improvements to readthedocs documentation [\#1853](https://github.com/bigdatagenomics/adam/issues/1853)
- add filterByOverlappingRegion(query: ReferenceRegion) to R and python APIs [\#1852](https://github.com/bigdatagenomics/adam/issues/1852)
- Support adding VCF header lines from Python [\#1840](https://github.com/bigdatagenomics/adam/issues/1840)
- Support loadIndexedBam from Python [\#1836](https://github.com/bigdatagenomics/adam/issues/1836)
- Add link to awesome list of applications that extend ADAM [\#1832](https://github.com/bigdatagenomics/adam/issues/1832)
- loadIndexed bam lazily throws Exception if index does not exist [\#1830](https://github.com/bigdatagenomics/adam/issues/1830)
- OAuth credentials for Github in Coveralls configuration are no longer valid [\#1829](https://github.com/bigdatagenomics/adam/issues/1829)
- base counts per position [\#1825](https://github.com/bigdatagenomics/adam/issues/1825)
- Issues loading BAM files in Google FS [\#1816](https://github.com/bigdatagenomics/adam/issues/1816)
- Error when writing a vcf file to Parquet [\#1810](https://github.com/bigdatagenomics/adam/issues/1810)
- transformAlignments cannot repartition files [\#1808](https://github.com/bigdatagenomics/adam/issues/1808)
- GenotypeRDD should support `toVariants` method [\#1806](https://github.com/bigdatagenomics/adam/issues/1806)
- Add support for python and R in Homebrew formula [\#1796](https://github.com/bigdatagenomics/adam/issues/1796)
- Add `transformVariantContexts` or similar to cli [\#1793](https://github.com/bigdatagenomics/adam/issues/1793)
- Issue while using Sorting option [\#1791](https://github.com/bigdatagenomics/adam/issues/1791)
- Issue with adam2vcf [\#1787](https://github.com/bigdatagenomics/adam/issues/1787)
- Remove explicit `<compile>` scopes from submodule POMs [\#1786](https://github.com/bigdatagenomics/adam/issues/1786)
- java.nio.file.ProviderNotFoundException (Provider "s3" not found) [\#1732](https://github.com/bigdatagenomics/adam/issues/1732)
- Accessing GenomicRDD join functions in python [\#1728](https://github.com/bigdatagenomics/adam/issues/1728)
- ArrayIndexOutOfBoundsException in PhredUtils$.phredToSuccessProbability [\#1714](https://github.com/bigdatagenomics/adam/issues/1714)
- Add ability to specify region bounds to pipe command [\#1707](https://github.com/bigdatagenomics/adam/issues/1707)
- Unable to run pyadam, SQLException: Failed to start database 'metastore_db' [\#1666](https://github.com/bigdatagenomics/adam/issues/1666)
- SAMFormatException: Unrecognized tag type: ^@ [\#1657](https://github.com/bigdatagenomics/adam/issues/1657)
- IndexOutOfBoundsException in BAMInputFormat.getSplits [\#1656](https://github.com/bigdatagenomics/adam/issues/1656)
- overlaps considers that Strand.FORWARD cannot overlap with Strand.INDEPENDENT [\#1650](https://github.com/bigdatagenomics/adam/issues/1650)
- migration converters [\#1629](https://github.com/bigdatagenomics/adam/issues/1629)
- RFC: Removing Spark 1.x, Scala 2.10 support in 0.24.0 release [\#1597](https://github.com/bigdatagenomics/adam/issues/1597)
- Eliminate unused ConcreteADAMRDDFunctions class [\#1580](https://github.com/bigdatagenomics/adam/issues/1580)
- Add set theory/statistics packages to ADAM [\#1533](https://github.com/bigdatagenomics/adam/issues/1533)
- Evaluate Apache Carbondata INDEXED column store file format for genomics [\#1527](https://github.com/bigdatagenomics/adam/issues/1527)
- Stranded vs unstranded in getReferenceRegions() for features [\#1513](https://github.com/bigdatagenomics/adam/issues/1513)
- Question:How to tranform a line of sam to AlignmentRecord? [\#1425](https://github.com/bigdatagenomics/adam/issues/1425)
- Excessive compilation warnings about multiple scala libraries [\#695](https://github.com/bigdatagenomics/adam/issues/695)
- Support Hive-style partitioning [\#651](https://github.com/bigdatagenomics/adam/issues/651)
**Merged and closed pull requests:**
- [ADAM-1964] Lower point where phred conversions are done using log code. [\#1965](https://github.com/bigdatagenomics/adam/pull/1965) ([fnothaft](https://github.com/fnothaft))
- Add utility methods for adam-shell. [\#1958](https://github.com/bigdatagenomics/adam/pull/1958) ([heuermh](https://github.com/heuermh))
- [ADAM-1955] Add support for downsampling during recalibration table generation [\#1963](https://github.com/bigdatagenomics/adam/pull/1963) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1957] Don't initialize missing likelihoods to MinValue. [\#1961](https://github.com/bigdatagenomics/adam/pull/1961) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1959] Support VCF rows at position 0. [\#1960](https://github.com/bigdatagenomics/adam/pull/1960) ([fnothaft](https://github.com/fnothaft))
- [ADAM-651] Implement Hive-style partitioning by genomic range of Parquet backed datasets [\#1948](https://github.com/bigdatagenomics/adam/pull/1948) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1914] Python profile needs to be specified for egg to be in distribution. [\#1946](https://github.com/bigdatagenomics/adam/pull/1946) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1917] Delete dependency on fulltoc. [\#1944](https://github.com/bigdatagenomics/adam/pull/1944) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1917] Try 3: fix Sphinx fulltoc. [\#1943](https://github.com/bigdatagenomics/adam/pull/1943) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1917] Set Sphinx version in requirements.txt. [\#1942](https://github.com/bigdatagenomics/adam/pull/1942) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1917] Set minimal Sphinx version for Readthedocs build. [\#1941](https://github.com/bigdatagenomics/adam/pull/1941) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1939] Allow validation stringency to waive off FLAG arrays. [\#1940](https://github.com/bigdatagenomics/adam/pull/1940) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1915] Bump to Hadoop-BAM 7.9.2. [\#1938](https://github.com/bigdatagenomics/adam/pull/1938) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1934] Clip phred values to 3233, instead of Int.MaxValue. [\#1936](https://github.com/bigdatagenomics/adam/pull/1936) ([fnothaft](https://github.com/fnothaft))
- Ignore VCF INFO fields with number=G when stringency=LENIENT [\#1935](https://github.com/bigdatagenomics/adam/pull/1935) ([jpdna](https://github.com/jpdna))
- [ADAM-1931] Bump to Spark 2.3.0. [\#1933](https://github.com/bigdatagenomics/adam/pull/1933) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1840] Support adding VCF header lines from Python. [\#1930](https://github.com/bigdatagenomics/adam/pull/1930) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1927] Increase visibility for util.FileExtensions for use downstream. [\#1929](https://github.com/bigdatagenomics/adam/pull/1929) ([heuermh](https://github.com/heuermh))
- [ADAM-1925] Reduce logging level for ADAMKryoRegistrator. [\#1928](https://github.com/bigdatagenomics/adam/pull/1928) ([heuermh](https://github.com/heuermh))
- [ADAM-1923] Revert 1eed8e8 [\#1926](https://github.com/bigdatagenomics/adam/pull/1926) ([fnothaft](https://github.com/fnothaft))
- Use SparkFiles.getRootDirectory in local mode. [\#1924](https://github.com/bigdatagenomics/adam/pull/1924) ([heuermh](https://github.com/heuermh))
- [ADAM-651] Implement Hive-style partitioning by genomic range of Parquet backed datasets [\#1922](https://github.com/bigdatagenomics/adam/pull/1922) ([jpdna](https://github.com/jpdna))
- Make Spark SQL APIs supported across all types [\#1921](https://github.com/bigdatagenomics/adam/pull/1921) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1909] Refactor pipe cmd parameter from String to Seq[String]. [\#1920](https://github.com/bigdatagenomics/adam/pull/1920) ([heuermh](https://github.com/heuermh))
- Add Google Cloud documentation [\#1918](https://github.com/bigdatagenomics/adam/pull/1918) ([Georgehe4](https://github.com/Georgehe4))
- [ADAM-1917] Load sphinxcontrib.fulltoc with imp.load_sources. [\#1916](https://github.com/bigdatagenomics/adam/pull/1916) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1912] Add asSingleFile, disableFastConcat to adam2fasta/q. [\#1913](https://github.com/bigdatagenomics/adam/pull/1913) ([heuermh](https://github.com/heuermh))
- [ADAM-651] Hive-style partitioning of parquet files by genomic position [\#1911](https://github.com/bigdatagenomics/adam/pull/1911) ([jpdna](https://github.com/jpdna))
- Minor unit test/style fixes. [\#1910](https://github.com/bigdatagenomics/adam/pull/1910) ([heuermh](https://github.com/heuermh))
- [ADAM-1907] Bump to HTSJDK 2.13.2. [\#1908](https://github.com/bigdatagenomics/adam/pull/1908) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1882] Don't abort adam-submit if ADAM_HOME is set. [\#1905](https://github.com/bigdatagenomics/adam/pull/1905) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1806] Add toVariants conversion from GenotypeRDD. [\#1904](https://github.com/bigdatagenomics/adam/pull/1904) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1882] Return true if ADAM_HOME is set, not exit 0. [\#1903](https://github.com/bigdatagenomics/adam/pull/1903) ([heuermh](https://github.com/heuermh))
- [ADAM-1900] Close stream after reading VCF header. [\#1901](https://github.com/bigdatagenomics/adam/pull/1901) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1898] Support converting INFO fields set to empty ('.'). [\#1899](https://github.com/bigdatagenomics/adam/pull/1899) ([fnothaft](https://github.com/fnothaft))
- Add Kryo registration for two classes required for Spark 2.3.0. [\#1897](https://github.com/bigdatagenomics/adam/pull/1897) ([jpdna](https://github.com/jpdna))
- [ADAM-1853] Various improvements to readthedocs documentation. [\#1893](https://github.com/bigdatagenomics/adam/pull/1893) ([heuermh](https://github.com/heuermh))
- [ADAM-1889][ADAM-1884] updated ReferenceRegion in python [\#1892](https://github.com/bigdatagenomics/adam/pull/1892) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1889] Run R/Python tests. [\#1890](https://github.com/bigdatagenomics/adam/pull/1890) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1886] fix for pyadam to recognize >1 egg file [\#1887](https://github.com/bigdatagenomics/adam/pull/1887) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1883] Python and R caching [\#1885](https://github.com/bigdatagenomics/adam/pull/1885) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1875] Add ability to timeout a piped command. [\#1881](https://github.com/bigdatagenomics/adam/pull/1881) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1871] Fix print call that broke python 3 support. [\#1880](https://github.com/bigdatagenomics/adam/pull/1880) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1832] Use awesome list style and link to bigdatagenomics/awesome-adam. [\#1879](https://github.com/bigdatagenomics/adam/pull/1879) ([heuermh](https://github.com/heuermh))
- [ADAM-651] Hive-style partitioning of parquet files by genomic position [\#1878](https://github.com/bigdatagenomics/adam/pull/1878) ([jpdna](https://github.com/jpdna))
- [ADAM-1874] Dedupe samples when loading VCFs. [\#1876](https://github.com/bigdatagenomics/adam/pull/1876) ([fnothaft](https://github.com/fnothaft))
- Fixes Coverage python API and adds tests [\#1870](https://github.com/bigdatagenomics/adam/pull/1870) ([akmorrow13](https://github.com/akmorrow13))
- added filterByOverlappingRegion for python [\#1869](https://github.com/bigdatagenomics/adam/pull/1869) ([akmorrow13](https://github.com/akmorrow13))
- Add command line option for populating nested variant.annotation field in Genotype records. [\#1865](https://github.com/bigdatagenomics/adam/pull/1865) ([heuermh](https://github.com/heuermh))
- Hive partitioned(v4) rebased [\#1864](https://github.com/bigdatagenomics/adam/pull/1864) ([jpdna](https://github.com/jpdna))
- [ADAM-1597] Move to Scala 2.11 and Spark 2.x. [\#1861](https://github.com/bigdatagenomics/adam/pull/1861) ([heuermh](https://github.com/heuermh))
- [ADAM-1857] Fix formatting error due to forward slashes. [\#1860](https://github.com/bigdatagenomics/adam/pull/1860) ([heuermh](https://github.com/heuermh))
- [ADAM-1858] Use getattr instead of Class.forName from python API. [\#1859](https://github.com/bigdatagenomics/adam/pull/1859) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1836] Adds loadIndexedBam API to Python and Java. [\#1837](https://github.com/bigdatagenomics/adam/pull/1837) ([fnothaft](https://github.com/fnothaft))
- Added check for bam index files in loadIndexedBam [\#1831](https://github.com/bigdatagenomics/adam/pull/1831) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1793] Adding vcf2adam and adam2vcf that handle separate variant and genotype data. [\#1794](https://github.com/bigdatagenomics/adam/pull/1794) ([heuermh](https://github.com/heuermh))
- added adam notebook [\#1778](https://github.com/bigdatagenomics/adam/pull/1778) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1666] SQLContext creation fix for Spark 2.x [\#1777](https://github.com/bigdatagenomics/adam/pull/1777) ([akmorrow13](https://github.com/akmorrow13))
- Add optional accumulator for VCF header lines to VCFOutFormatter. [\#1727](https://github.com/bigdatagenomics/adam/pull/1727) ([heuermh](https://github.com/heuermh))
- add hive style partitioning for contigName [\#1620](https://github.com/bigdatagenomics/adam/pull/1620) ([jpdna](https://github.com/jpdna))
- Add loadReadsFromSamString function into ADAMContext [\#1434](https://github.com/bigdatagenomics/adam/pull/1434) ([xubo245](https://github.com/xubo245))
### Version 0.23.0 ###
**Closed issues:**
- Readthedocs build error [\#1854](https://github.com/bigdatagenomics/adam/issues/1854)
- Add pip release to release scripts [\#1847](https://github.com/bigdatagenomics/adam/issues/1847)
- Publish scaladoc script still attempts to build markdown docs [\#1845](https://github.com/bigdatagenomics/adam/issues/1845)
- Allow variant annotations to be loaded into genotypes [\#1838](https://github.com/bigdatagenomics/adam/issues/1838)
- Specify correct extensions for SAM/BAM output [\#1834](https://github.com/bigdatagenomics/adam/issues/1834)
- Fix link anchors and other issues in readthedocs [\#1822](https://github.com/bigdatagenomics/adam/issues/1822)
- Sphinx fulltoc is not included [\#1821](https://github.com/bigdatagenomics/adam/issues/1821)
- Readme link to bigdatagenomics/lime 404s [\#1819](https://github.com/bigdatagenomics/adam/issues/1819)
- Bump to Hadoop-BAM 7.9.1 [\#1817](https://github.com/bigdatagenomics/adam/issues/1817)
- LoadVariants Header Format [\#1815](https://github.com/bigdatagenomics/adam/issues/1815)
- Right and Left Outer Shuffle Region Join don't match [\#1813](https://github.com/bigdatagenomics/adam/issues/1813)
- Pipe command can fail with empty partitions [\#1807](https://github.com/bigdatagenomics/adam/issues/1807)
- adam files with outdated formats throw FileNotFoundException [\#1804](https://github.com/bigdatagenomics/adam/issues/1804)
- Move GenomicRDD.writeTextRDD outside of GenomicRDD [\#1803](https://github.com/bigdatagenomics/adam/issues/1803)
- find-adam-assembly fails to recognize more than 1 jar [\#1801](https://github.com/bigdatagenomics/adam/issues/1801)
- tests/testthat.R failed on git head [\#1799](https://github.com/bigdatagenomics/adam/issues/1799)
- Run python and R tests conditionally in build [\#1795](https://github.com/bigdatagenomics/adam/issues/1795)
- scala-lang should be a provided dependency [\#1789](https://github.com/bigdatagenomics/adam/issues/1789)
- loadIndexedBam does an unnecessary union [\#1784](https://github.com/bigdatagenomics/adam/issues/1784)
- Release bdgenomics.adam R package on CRAN [\#1783](https://github.com/bigdatagenomics/adam/issues/1783)
- Issue with transformVariant // Adam to vcf [\#1782](https://github.com/bigdatagenomics/adam/issues/1782)
- Add code of conduct [\#1779](https://github.com/bigdatagenomics/adam/issues/1779)
- Reinstantiation of SQLContext in pyadam ADAMContext [\#1774](https://github.com/bigdatagenomics/adam/issues/1774)
- Genotypes should only contain the core variant fields [\#1770](https://github.com/bigdatagenomics/adam/issues/1770)
- Add SingleFASTQInFormatter [\#1768](https://github.com/bigdatagenomics/adam/issues/1768)
- INDEL realigner can emit negative partition IDs [\#1763](https://github.com/bigdatagenomics/adam/issues/1763)
- Request for a new release [\#1762](https://github.com/bigdatagenomics/adam/issues/1762)
- INDEL realigner generates targets for reads with more than 1 INDEL [\#1753](https://github.com/bigdatagenomics/adam/issues/1753)
- Fragment Issue [\#1752](https://github.com/bigdatagenomics/adam/issues/1752)
- Variant Caller!!! [\#1751](https://github.com/bigdatagenomics/adam/issues/1751)
- Spark Version!! [\#1750](https://github.com/bigdatagenomics/adam/issues/1750)
- ReferenceRegion.subtract eliminating valid regions [\#1747](https://github.com/bigdatagenomics/adam/issues/1747)
- New Shuffle Join Implementation - Left Outer + Group By Left [\#1745](https://github.com/bigdatagenomics/adam/issues/1745)
- command failure after build success [\#1744](https://github.com/bigdatagenomics/adam/issues/1744)
- Recalibrate_base_Qualities [\#1743](https://github.com/bigdatagenomics/adam/issues/1743)
- Standardize regionFn for ShuffleJoin returned objects [\#1740](https://github.com/bigdatagenomics/adam/issues/1740)
- Shuffle, Broadcast Joins with threshold [\#1739](https://github.com/bigdatagenomics/adam/issues/1739)
- Adam on Spark 2.1 [\#1738](https://github.com/bigdatagenomics/adam/issues/1738)
- Opening up permission on GenericGenomicRDD constructor [\#1735](https://github.com/bigdatagenomics/adam/issues/1735)
- Consistency on ShuffleRegionJoin returns [\#1734](https://github.com/bigdatagenomics/adam/issues/1734)
- vcf2adam support [\#1731](https://github.com/bigdatagenomics/adam/issues/1731)
- Cloud-scale BWA MEM [\#1730](https://github.com/bigdatagenomics/adam/issues/1730)
- Aligned Human Genome couldn't convert to Adam [\#1729](https://github.com/bigdatagenomics/adam/issues/1729)
- Mark Duplicates [\#1726](https://github.com/bigdatagenomics/adam/issues/1726)
- Genomics Pipeline [\#1724](https://github.com/bigdatagenomics/adam/issues/1724)
- .fastq Alignment [\#1723](https://github.com/bigdatagenomics/adam/issues/1723)
- Is it correct Adam file [\#1720](https://github.com/bigdatagenomics/adam/issues/1720)
- .fastQ to .adam [\#1718](https://github.com/bigdatagenomics/adam/issues/1718)
- Unable to create .adam from .sam [\#1717](https://github.com/bigdatagenomics/adam/issues/1717)
- Add adam- prefix to distribution module name [\#1716](https://github.com/bigdatagenomics/adam/issues/1716)
- Python load methods don't have ability to specify validation stringency [\#1715](https://github.com/bigdatagenomics/adam/issues/1715)
- NPE when trying to map *loadVariants* over RDD [\#1713](https://github.com/bigdatagenomics/adam/issues/1713)
- Add left normalization of INDELs as an RDD level primitive [\#1709](https://github.com/bigdatagenomics/adam/issues/1709)
- Allow validation stringency to be set in AnySAMOutFormatter [\#1703](https://github.com/bigdatagenomics/adam/issues/1703)
- InterleavedFastqInFormatter should sort by readInFragment [\#1702](https://github.com/bigdatagenomics/adam/issues/1702)
- Allow silencing the # of reads in fragment warning in InterleavedFastqInFormatter [\#1701](https://github.com/bigdatagenomics/adam/issues/1701)
- GenomicRDD.toXxx method names should be consistent [\#1699](https://github.com/bigdatagenomics/adam/issues/1699)
- Exception thrown in VariantContextConverter.formatAllelicDepth despite SILENT validation stringency [\#1695](https://github.com/bigdatagenomics/adam/issues/1695)
- Make GenomicRDD.toString more adam-shell friendly [\#1694](https://github.com/bigdatagenomics/adam/issues/1694)
- Add adam-shell friendly VariantContextRDD.saveAsVcf method [\#1693](https://github.com/bigdatagenomics/adam/issues/1693)
- change bdgenomics.adam package name for adam-python to bdg-adam [\#1691](https://github.com/bigdatagenomics/adam/issues/1691)
- Conflict in bdg-formats dependency version due to org.hammerlab:genomic-loci [\#1688](https://github.com/bigdatagenomics/adam/issues/1688)
- Convert and store variant quality field. [\#1682](https://github.com/bigdatagenomics/adam/issues/1682)
- Region join shows non-determinism [\#1680](https://github.com/bigdatagenomics/adam/issues/1680)
- Shuffle region join throws multimapped exception for unmapped reads [\#1679](https://github.com/bigdatagenomics/adam/issues/1679)
- Push validation checks down to INFO/FORMAT fields [\#1676](https://github.com/bigdatagenomics/adam/issues/1676)
- IndexOutOfBounds thrown when saving gVCF with no likelihoods [\#1673](https://github.com/bigdatagenomics/adam/issues/1673)
- Generate docs from R API for distribution [\#1672](https://github.com/bigdatagenomics/adam/issues/1672)
- Support loading a subset of VCF fields [\#1670](https://github.com/bigdatagenomics/adam/issues/1670)
- Error with metadata: Multivalued flags are not supported for INFO lines [\#1669](https://github.com/bigdatagenomics/adam/issues/1669)
- Include bdg.adam-0.23.0.tar.gz in distribution tarballs [\#1668](https://github.com/bigdatagenomics/adam/issues/1668)
- Include bdgenomics.adam-0.23.0_SNAPSHOT-py2.7.egg in distribution tarball [\#1667](https://github.com/bigdatagenomics/adam/issues/1667)
- Add SUPPORT.md file to complement CONTRIBUTING.md [\#1664](https://github.com/bigdatagenomics/adam/issues/1664)
- Can't merge BAM files containing the same sample [\#1663](https://github.com/bigdatagenomics/adam/issues/1663)
- Incorrect README.md kmer.scala loadAliments method parameter name [\#1662](https://github.com/bigdatagenomics/adam/issues/1662)
- Add performance benchmarks similar to Samtools CRAM benchmarking page [\#1661](https://github.com/bigdatagenomics/adam/issues/1661)
- Transient bad GZIP header bug when loading BGZF FASTQ [\#1658](https://github.com/bigdatagenomics/adam/issues/1658)
- bdgenomics.adam vs bdg.adam for R/Python APIs [\#1655](https://github.com/bigdatagenomics/adam/issues/1655)
- Need adamR script [\#1649](https://github.com/bigdatagenomics/adam/issues/1649)
- incorrect grep for assembly jars in bin/pyadam [\#1647](https://github.com/bigdatagenomics/adam/issues/1647)
- VariantRDD union creates multiple records for the same SNP ID [\#1644](https://github.com/bigdatagenomics/adam/issues/1644)
- S3 access documentation [\#1643](https://github.com/bigdatagenomics/adam/issues/1643)
- Algorithms docs formatting [\#1639](https://github.com/bigdatagenomics/adam/issues/1639)
- Building downstream apps docs reformatting [\#1638](https://github.com/bigdatagenomics/adam/issues/1638)
- FastqInputFormat.FILE_SPLITTABLE in conf not getting passed properly [\#1635](https://github.com/bigdatagenomics/adam/issues/1635)
- Add benchmarks to documentation [\#1634](https://github.com/bigdatagenomics/adam/issues/1634)
- Intro docs contain outdated/incompatible code [\#1633](https://github.com/bigdatagenomics/adam/issues/1633)
- Intro docs missing a number of active projects [\#1632](https://github.com/bigdatagenomics/adam/issues/1632)
- Installation instructions for Homebrew missing from documentation [\#1631](https://github.com/bigdatagenomics/adam/issues/1631)
- Architecture section is missing from docs [\#1630](https://github.com/bigdatagenomics/adam/issues/1630)
- Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> with javac [\#1625](https://github.com/bigdatagenomics/adam/issues/1625)
- ProcessingStep missing from adam-codegen [\#1623](https://github.com/bigdatagenomics/adam/issues/1623)
- Add ADAM recipe to bioconda [\#1618](https://github.com/bigdatagenomics/adam/issues/1618)
- adam-submit cannot find assembly jar if installed as symlink [\#1616](https://github.com/bigdatagenomics/adam/issues/1616)
- Expose transform/transmute in Java/Python/R [\#1615](https://github.com/bigdatagenomics/adam/issues/1615)
- Expose VariantContextRDD in R/Python [\#1614](https://github.com/bigdatagenomics/adam/issues/1614)
- Expose pipe API from Python/R [\#1611](https://github.com/bigdatagenomics/adam/issues/1611)
- Serialization issue with TwoBitFile [\#1610](https://github.com/bigdatagenomics/adam/issues/1610)
- Snapshot Distribution Does not include jar files [\#1607](https://github.com/bigdatagenomics/adam/issues/1607)
- ManualRegionPartitioner is broken for ParallelFileMerger codepath [\#1602](https://github.com/bigdatagenomics/adam/issues/1602)
- VariantRDD doesn't save partition map [\#1601](https://github.com/bigdatagenomics/adam/issues/1601)
- Scala copy method not supported in abstract classes such as AlignmentRecordRDD [\#1599](https://github.com/bigdatagenomics/adam/issues/1599)
- Interleaved FASTQ recognizes only /1 suffix pattern [\#1589](https://github.com/bigdatagenomics/adam/issues/1589)
- Use empty sequence dictionary when loading features [\#1588](https://github.com/bigdatagenomics/adam/issues/1588)
- New Illumina FASTQ spec adds metadata to read name line [\#1585](https://github.com/bigdatagenomics/adam/issues/1585)
- first run of ADAM [\#1582](https://github.com/bigdatagenomics/adam/issues/1582)
- Add unit test coverage for BED12 parser and writer [\#1579](https://github.com/bigdatagenomics/adam/issues/1579)
- Spark 1.x Scala 2.10 snapshot artifacts missing since 31 March 2017 [\#1578](https://github.com/bigdatagenomics/adam/issues/1578)
- Unable to save GenomicRDDs after a join. [\#1576](https://github.com/bigdatagenomics/adam/issues/1576)
- Add filterBySequenceDictionary to GenomicRDD [\#1575](https://github.com/bigdatagenomics/adam/issues/1575)
- Unaligned Trait does nothing [\#1573](https://github.com/bigdatagenomics/adam/issues/1573)
- Bump to bdg-formats 0.11.1 [\#1570](https://github.com/bigdatagenomics/adam/issues/1570)
- PhredUtils conversion to log probabilities has insufficient resolution for PLs [\#1569](https://github.com/bigdatagenomics/adam/issues/1569)
- Reference model import code is borked [\#1568](https://github.com/bigdatagenomics/adam/issues/1568)
- SequenceDictionary vs Feature[RDD] of reference length features [\#1567](https://github.com/bigdatagenomics/adam/issues/1567)
- giab-NA12878 truth_small_variants.vcf.gz header issues [\#1566](https://github.com/bigdatagenomics/adam/issues/1566)
- VCF header read from stream ignored in VCFOutFormatter [\#1564](https://github.com/bigdatagenomics/adam/issues/1564)
- VCF genotype Number=A attribute throws ArrayIndexOutOfBoundsException [\#1562](https://github.com/bigdatagenomics/adam/issues/1562)
- Save compressed single file VCF via HadoopBAM [\#1554](https://github.com/bigdatagenomics/adam/issues/1554)
- bucketing strategy [\#1553](https://github.com/bigdatagenomics/adam/issues/1553)
- Is parquet using delta encoding for positions? [\#1552](https://github.com/bigdatagenomics/adam/issues/1552)
- Export to VCF does not include symbolic non-ref if site has a called alt [\#1551](https://github.com/bigdatagenomics/adam/issues/1551)
- Refactor filterByOverlappingRegions not to require a List [\#1549](https://github.com/bigdatagenomics/adam/issues/1549)
- Move docs to Sphinx/pure Markdown [\#1548](https://github.com/bigdatagenomics/adam/issues/1548)
- java.lang.IncompatibleClassChangeError: Implementing class [\#1544](https://github.com/bigdatagenomics/adam/issues/1544)
- Support locus predicate in `TransformAlignments` [\#1539](https://github.com/bigdatagenomics/adam/issues/1539)
- Visibility from Java, jrdd has private access in AvroGenomicRDD [\#1538](https://github.com/bigdatagenomics/adam/issues/1538)
- Rename o.b.adam.apis.java package to o.b.adam.api.java [\#1537](https://github.com/bigdatagenomics/adam/issues/1537)
- VCF header genotype reserved key FT cardinality clobbered by htsjdk [\#1535](https://github.com/bigdatagenomics/adam/issues/1535)
- Compute a SequenceDictionary from a *.genome file [\#1534](https://github.com/bigdatagenomics/adam/issues/1534)
- Queryname sorted check should check for queryname grouped as well [\#1530](https://github.com/bigdatagenomics/adam/issues/1530)
- Bump to bdg-formats 0.11.0 [\#1520](https://github.com/bigdatagenomics/adam/issues/1520)
- Move to Spark 2.2, Parquet 1.8.2 [\#1517](https://github.com/bigdatagenomics/adam/issues/1517)
- Minor refactor for TreeRegionJoin for consistency [\#1514](https://github.com/bigdatagenomics/adam/issues/1514)
- Allow +Inf and -Inf Float values when reading VCF [\#1512](https://github.com/bigdatagenomics/adam/issues/1512)
- SparkFiles temp directory path should be accessible as a variable [\#1510](https://github.com/bigdatagenomics/adam/issues/1510)
- SparkFiles.get expects just the filename [\#1509](https://github.com/bigdatagenomics/adam/issues/1509)
- Split apart #1324 [\#1507](https://github.com/bigdatagenomics/adam/issues/1507)
- Where can I find "Phred-scaled quality score" (QUAL)? [\#1506](https://github.com/bigdatagenomics/adam/issues/1506)
- Alignment Record sort is not consistent with samtools [\#1504](https://github.com/bigdatagenomics/adam/issues/1504)
- Sequence dictionary records in TwoBitFile are not stable [\#1502](https://github.com/bigdatagenomics/adam/issues/1502)
- Move coverage counter over to Dataset API [\#1501](https://github.com/bigdatagenomics/adam/issues/1501)
- Allow users to set the minimum partition count across all load methods [\#1500](https://github.com/bigdatagenomics/adam/issues/1500)
- Enable reuse of broadcast object across broadcast region joins [\#1499](https://github.com/bigdatagenomics/adam/issues/1499)
- Take union across genomic RDDs [\#1497](https://github.com/bigdatagenomics/adam/issues/1497)
- Adam files created by vcf2adam is not recognizable [\#1496](https://github.com/bigdatagenomics/adam/issues/1496)
- Scalatest log output disappears with Maven 3.5.0 [\#1495](https://github.com/bigdatagenomics/adam/issues/1495)
- ArrayOutOfBoundsException in vcf2adam (spark2_2.11-0.22.0) on UK10K VCFs (VCFv4.1) [\#1494](https://github.com/bigdatagenomics/adam/issues/1494)
- ReferenceRegion overlaps and covers returns false if overlap is 1 [\#1492](https://github.com/bigdatagenomics/adam/issues/1492)
- Provide asSingleFile parameter for saveAsFastq and related [\#1490](https://github.com/bigdatagenomics/adam/issues/1490)
- Min Phred score gets bumped by 33 twice in BQSR [\#1488](https://github.com/bigdatagenomics/adam/issues/1488)
- Should throw error when BAM header load fails [\#1486](https://github.com/bigdatagenomics/adam/issues/1486)
- Default value for reads.toCoverage(collapse) should be false [\#1483](https://github.com/bigdatagenomics/adam/issues/1483)
- Refactor ADAMContext loadXxx methods for consistency [\#1481](https://github.com/bigdatagenomics/adam/issues/1481)
- loadGenotypes three time [\#1480](https://github.com/bigdatagenomics/adam/issues/1480)
- Fall back to sequential concat when HDFS concat fails [\#1478](https://github.com/bigdatagenomics/adam/issues/1478)
- VCF line with `.` ALT gets dropped [\#1476](https://github.com/bigdatagenomics/adam/issues/1476)
- ADAM works on Cloudera but does NOT work on MAPR [\#1475](https://github.com/bigdatagenomics/adam/issues/1475)
- Clean up ReferenceRegion.scala [\#1474](https://github.com/bigdatagenomics/adam/issues/1474)
- Allow joins on regions that are within a threshold (instead of requiring overlap) [\#1473](https://github.com/bigdatagenomics/adam/issues/1473)
- FeatureRDD.toCoverage throws NullPointerException when there is no coverage information [\#1471](https://github.com/bigdatagenomics/adam/issues/1471)
- Add quality score binner [\#1462](https://github.com/bigdatagenomics/adam/issues/1462)
- Splittable compression and FASTQ [\#1457](https://github.com/bigdatagenomics/adam/issues/1457)
- Don't convert .{different-type}.adam in loadAlignments and loadFragments [\#1456](https://github.com/bigdatagenomics/adam/issues/1456)
- New primitives for adam-core [\#1454](https://github.com/bigdatagenomics/adam/issues/1454)
- Port over code for populating SequenceDictionaries from .dict files [\#1449](https://github.com/bigdatagenomics/adam/issues/1449)
- Ignore failed push to Coveralls during CI builds [\#1444](https://github.com/bigdatagenomics/adam/issues/1444)
- No asSingleFile parameter for saveAsFasta in NucleotideContigFragmentRDD [\#1438](https://github.com/bigdatagenomics/adam/issues/1438)
- shufflejoin and ArrayIndexOutOfBoundsException [\#1436](https://github.com/bigdatagenomics/adam/issues/1436)
- Document using ADAM snapshot [\#1432](https://github.com/bigdatagenomics/adam/issues/1432)
- Improve metrics coverage across ADAMContext load methods [\#1428](https://github.com/bigdatagenomics/adam/issues/1428)
- loadReferenceFile missing from Java API [\#1421](https://github.com/bigdatagenomics/adam/issues/1421)
- loadCoverage missing from Java API [\#1420](https://github.com/bigdatagenomics/adam/issues/1420)
- Question: How to get paired-end alignemntRecord like RDD[AlignmentRecord, AlignmentRecordRDD]? [\#1419](https://github.com/bigdatagenomics/adam/issues/1419)
- Clean up possibly unused methods in Projection [\#1417](https://github.com/bigdatagenomics/adam/issues/1417)
- Problem loading SNPeff annotated VCF [\#1390](https://github.com/bigdatagenomics/adam/issues/1390)
- RecordGroupDictionary should support `isEmpty` [\#1380](https://github.com/bigdatagenomics/adam/issues/1380)
- Get rid of mutable collection transformations in ShuffleRegionJoin [\#1379](https://github.com/bigdatagenomics/adam/issues/1379)
- Add tab5/6 as native output format for AlignmentRecordRDD [\#1377](https://github.com/bigdatagenomics/adam/issues/1377)
- ValidationStringency in MDTagging should apply to reads on unknown references [\#1365](https://github.com/bigdatagenomics/adam/issues/1365)
- Assembly final name doesn't include spark2 for Spark 2.x builds [\#1361](https://github.com/bigdatagenomics/adam/issues/1361)
- Merge reads2fragments and fragments2reads into a single CLI [\#1359](https://github.com/bigdatagenomics/adam/issues/1359)
- Investigate failures to load ExAC.0.3.GRCh38.vcf variants [\#1351](https://github.com/bigdatagenomics/adam/issues/1351)
- adam-shell does not allow additional jars via Spark jars argument [\#1349](https://github.com/bigdatagenomics/adam/issues/1349)
- Loading GZipped VCF returns an empty RDD [\#1333](https://github.com/bigdatagenomics/adam/issues/1333)
- Bump Spark 2 build to Spark 2.1.0 [\#1330](https://github.com/bigdatagenomics/adam/issues/1330)
- Rename Transform command TransformAlignments or similar [\#1328](https://github.com/bigdatagenomics/adam/issues/1328)
- Replace ADAM2Vcf and Vcf2ADAM commands with TransformGenotypes and TransformVariants [\#1327](https://github.com/bigdatagenomics/adam/issues/1327)
- FeatureRDD instantiation tries to cache the RDD [\#1321](https://github.com/bigdatagenomics/adam/issues/1321)
- Repository for Pipe API wrappers for bioinformatics tools [\#1314](https://github.com/bigdatagenomics/adam/issues/1314)
- Trying to get Spark pipeline working with slightly out of date code. [\#1313](https://github.com/bigdatagenomics/adam/issues/1313)
- Support for gVCF merging and genotyping (e.g. CombineGVCFs and GenotypeGVCFs) [\#1312](https://github.com/bigdatagenomics/adam/issues/1312)
- Support for read alignment and variant calling in Adam? (e.g. BWA + Freebayes) [\#1311](https://github.com/bigdatagenomics/adam/issues/1311)
- Don't include log4j.properties in published JAR [\#1300](https://github.com/bigdatagenomics/adam/issues/1300)
- Removing ProgramRecords info when saving data to sam/bam? [\#1257](https://github.com/bigdatagenomics/adam/issues/1257)
- ADAM on Slurm/LSF [\#1229](https://github.com/bigdatagenomics/adam/issues/1229)
- Maintaining sorted/partitioned knowledge [\#1216](https://github.com/bigdatagenomics/adam/issues/1216)
- Evaluate bdg-convert external conversion library proposal [\#1197](https://github.com/bigdatagenomics/adam/issues/1197)
- Port AMPCamp Tutorial over [\#1174](https://github.com/bigdatagenomics/adam/issues/1174)
- Top level WrappedRDD or similar abstraction [\#1173](https://github.com/bigdatagenomics/adam/issues/1173)
- GFF3 formatted features written as single file must include gff-version pragma [\#1169](https://github.com/bigdatagenomics/adam/issues/1169)
- Can probably eliminate sort in RealignIndels [\#1137](https://github.com/bigdatagenomics/adam/issues/1137)
- Load SV type info field - need for allele uniquness [\#1134](https://github.com/bigdatagenomics/adam/issues/1134)
- BroadcastRegionJoin is not a broadcast join [\#1110](https://github.com/bigdatagenomics/adam/issues/1110)
- AlignmentRecordRDD does not extend GenomicRDD per javac [\#1092](https://github.com/bigdatagenomics/adam/issues/1092)
- Add generic ReferenceRegion pushdown for parquet files [\#1047](https://github.com/bigdatagenomics/adam/issues/1047)
- Use of dataset api in ADAM [\#1018](https://github.com/bigdatagenomics/adam/issues/1018)
- Difference running markdups with and without projection [\#1014](https://github.com/bigdatagenomics/adam/issues/1014)
- ADAM to BAM conversion fails using relative path [\#1012](https://github.com/bigdatagenomics/adam/issues/1012)
- Refactor SequenceDictionary to use Contig instead of SequenceRecord [\#997](https://github.com/bigdatagenomics/adam/issues/997)
- NoSuchMethodError due to kryo minor-version mismatch [\#955](https://github.com/bigdatagenomics/adam/issues/955)
- Autogen field names in projection package [\#941](https://github.com/bigdatagenomics/adam/issues/941)
- Future of schemas in bdg-formats [\#925](https://github.com/bigdatagenomics/adam/issues/925)
- genotypeType for genotypes with multiple OtherAlt alleles? [\#897](https://github.com/bigdatagenomics/adam/issues/897)
- How to filter genotype RDD with FeatureRDD [\#890](https://github.com/bigdatagenomics/adam/issues/890)
- How to convert genotype DataFrame to VariantContext DataFrame / RDD [\#886](https://github.com/bigdatagenomics/adam/issues/886)
- R language package for Adam [\#882](https://github.com/bigdatagenomics/adam/issues/882)
- How to count genotypes with a 10 node Spark/Adam cluster faster than with BCFTools on a single machine? [\#879](https://github.com/bigdatagenomics/adam/issues/879)
- Ensure Java API is up-to-date with Scala API [\#855](https://github.com/bigdatagenomics/adam/issues/855)
- BroadcastRegionJoin fails with unmapped reads [\#821](https://github.com/bigdatagenomics/adam/issues/821)
- Resolve Fragment vs. SingleReadBucket [\#789](https://github.com/bigdatagenomics/adam/issues/789)
- Updating/Publishing the docs/ directory [\#774](https://github.com/bigdatagenomics/adam/issues/774)
- Next on empty iterator in BroadcastRegionJoin [\#661](https://github.com/bigdatagenomics/adam/issues/661)
- Cleanup code smell in sort work balancing code [\#635](https://github.com/bigdatagenomics/adam/issues/635)
- Provide low-impact alternative to `transform -repartition` for reducing partition size [\#594](https://github.com/bigdatagenomics/adam/issues/594)
- Create an ADAM Python API [\#538](https://github.com/bigdatagenomics/adam/issues/538)
- Migrate serialization libraries out of ADAM core [\#448](https://github.com/bigdatagenomics/adam/issues/448)
- Create standardized, interpretable exceptions for error reporting [\#420](https://github.com/bigdatagenomics/adam/issues/420)
- Build info/version info inside ADAM-generated files [\#188](https://github.com/bigdatagenomics/adam/issues/188)
**Merged and closed pull requests:**
- [ADAM-1854] Add requirements.txt file for RTD. [\#1856](https://github.com/bigdatagenomics/adam/pull/1856) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1783] Resolve check issues that block pushing to CRAN. [\#1849](https://github.com/bigdatagenomics/adam/pull/1849) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1847] Update ADAM scripts to support self-contained pip install. [\#1848](https://github.com/bigdatagenomics/adam/pull/1848) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1845] Only build and publish scaladocs in publish-scaladoc.sh. [\#1846](https://github.com/bigdatagenomics/adam/pull/1846) ([heuermh](https://github.com/heuermh))
- [ADAM-1843] Install sources before calling scala:doc in publish scaladoc [\#1844](https://github.com/bigdatagenomics/adam/pull/1844) ([fnothaft](https://github.com/fnothaft))
- Remove python and R profiles from release script [\#1842](https://github.com/bigdatagenomics/adam/pull/1842) ([heuermh](https://github.com/heuermh))
- [ADAM-1817] Bump to Hadoop-BAM 7.9.1. [\#1841](https://github.com/bigdatagenomics/adam/pull/1841) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1838] Make populating variant.annotation field in Genotype configurable [\#1839](https://github.com/bigdatagenomics/adam/pull/1839) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1834] Add proper extensions for SAM/BAM/CRAM output formats. [\#1835](https://github.com/bigdatagenomics/adam/pull/1835) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1822] Misc docs cleanup [\#1827](https://github.com/bigdatagenomics/adam/pull/1827) ([fnothaft](https://github.com/fnothaft))
- Added missing __init__.py for fulltoc. [\#1824](https://github.com/bigdatagenomics/adam/pull/1824) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1821] Add missing fulltoc for Sphinx documentation. [\#1823](https://github.com/bigdatagenomics/adam/pull/1823) ([fnothaft](https://github.com/fnothaft))
- Fix link to documentation [\#1820](https://github.com/bigdatagenomics/adam/pull/1820) ([nzachow](https://github.com/nzachow))
- [ADAM-1634] Add algorithm benchmarks to documentation. [\#1818](https://github.com/bigdatagenomics/adam/pull/1818) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1813] Delegate right outer shuffle region join to left OSRJ implementation. [\#1814](https://github.com/bigdatagenomics/adam/pull/1814) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1807] Check for empty partition when running a piped command. [\#1812](https://github.com/bigdatagenomics/adam/pull/1812) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1803] Refactor GenomicRDD.writeTextRdd to util.TextRddWriter. [\#1809](https://github.com/bigdatagenomics/adam/pull/1809) ([heuermh](https://github.com/heuermh))
- Added Filter error when file loaded does not match schema [\#1805](https://github.com/bigdatagenomics/adam/pull/1805) ([akmorrow13](https://github.com/akmorrow13))
- changed num_jars count [\#1802](https://github.com/bigdatagenomics/adam/pull/1802) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1795] Map -DskipTests=true to exec.skip for Python and R tests. [\#1800](https://github.com/bigdatagenomics/adam/pull/1800) ([heuermh](https://github.com/heuermh))
- [ADAM-1672] Use working directory for R devtools::document(). [\#1798](https://github.com/bigdatagenomics/adam/pull/1798) ([heuermh](https://github.com/heuermh))
- [ADAM-1789] Move scala-lang to provided scope. [\#1790](https://github.com/bigdatagenomics/adam/pull/1790) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1784] loadIndexedBam should pass the raw globbed path to Hadoop-BAM [\#1785](https://github.com/bigdatagenomics/adam/pull/1785) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1664] Add SUPPORT.md file to complement CONTRIBUTING.md. [\#1781](https://github.com/bigdatagenomics/adam/pull/1781) ([heuermh](https://github.com/heuermh))
- [ADAM-1779] Adding code of contact adapted from the Contributor Convenant, version 1.4. [\#1780](https://github.com/bigdatagenomics/adam/pull/1780) ([heuermh](https://github.com/heuermh))
- [ADAM-1661] Add file storage benchmarks. [\#1772](https://github.com/bigdatagenomics/adam/pull/1772) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1770] Genotype should only store core variant fields. [\#1771](https://github.com/bigdatagenomics/adam/pull/1771) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1768] Add InFormatter for unpaired FASTQ. [\#1769](https://github.com/bigdatagenomics/adam/pull/1769) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1643] Add S3 access documentation. [\#1767](https://github.com/bigdatagenomics/adam/pull/1767) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1763] Apply absolute value to destination partition in ModPartitioner [\#1766](https://github.com/bigdatagenomics/adam/pull/1766) ([fnothaft](https://github.com/fnothaft))
- Add R and Python into distribution artifacts [\#1765](https://github.com/bigdatagenomics/adam/pull/1765) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1655] Move R package to bdgenomics.adam. [\#1764](https://github.com/bigdatagenomics/adam/pull/1764) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1753] Only emit realignment targets for reads containing a single INDEL [\#1756](https://github.com/bigdatagenomics/adam/pull/1756) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1715] Support validation stringency in Python/R. [\#1755](https://github.com/bigdatagenomics/adam/pull/1755) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1680] Eliminate non-determinism in the ShuffleRegionJoin. [\#1754](https://github.com/bigdatagenomics/adam/pull/1754) ([fnothaft](https://github.com/fnothaft))
- update to _replaceRdd with tests [\#1749](https://github.com/bigdatagenomics/adam/pull/1749) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1747] Fixed subtract bug and tests [\#1748](https://github.com/bigdatagenomics/adam/pull/1748) ([devin-petersohn](https://github.com/devin-petersohn))
- [ADAM-1745] Adding LeftOuterShuffleRegionJoinAndGroupByLeft and tests [\#1746](https://github.com/bigdatagenomics/adam/pull/1746) ([devin-petersohn](https://github.com/devin-petersohn))
- Enabled thresholding for joins and standardized regionFn [\#1741](https://github.com/bigdatagenomics/adam/pull/1741) ([devin-petersohn](https://github.com/devin-petersohn))
- Making join return types consistent [\#1737](https://github.com/bigdatagenomics/adam/pull/1737) ([devin-petersohn](https://github.com/devin-petersohn))
- Opening up permissions on GenericGenomicRDD [\#1736](https://github.com/bigdatagenomics/adam/pull/1736) ([devin-petersohn](https://github.com/devin-petersohn))
- [ADAM-1716] Add adam- prefix to distribution module name. [\#1733](https://github.com/bigdatagenomics/adam/pull/1733) ([heuermh](https://github.com/heuermh))
- [ADAM-1695] Check for illegal genotype index after splitting multi-allelic variants. [\#1725](https://github.com/bigdatagenomics/adam/pull/1725) ([heuermh](https://github.com/heuermh))
- [ADAM-1517] Bump Parquet version in a manner compatible with Spark 2.2.x [\#1722](https://github.com/bigdatagenomics/adam/pull/1722) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1512] Support VCFs with +Inf/-Inf float values. [\#1721](https://github.com/bigdatagenomics/adam/pull/1721) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1709] Add ability to left normalize reads containing INDELs. [\#1711](https://github.com/bigdatagenomics/adam/pull/1711) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1691] Move bdgenomics.adam to use a namespace package. [\#1706](https://github.com/bigdatagenomics/adam/pull/1706) ([fnothaft](https://github.com/fnothaft))
- moved bdgenomics.adam package to bdgenomics-adam [\#1705](https://github.com/bigdatagenomics/adam/pull/1705) ([akmorrow13](https://github.com/akmorrow13))
- Misc cleanup needed for bigdatagenomics/cannoli#65 [\#1704](https://github.com/bigdatagenomics/adam/pull/1704) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1699] Make GenomicRDD.toXxx method names consistent. [\#1700](https://github.com/bigdatagenomics/adam/pull/1700) ([heuermh](https://github.com/heuermh))
- [ADAM-1694] Add short readable descriptions for toString in subclasses of GenomicRDD. [\#1698](https://github.com/bigdatagenomics/adam/pull/1698) ([heuermh](https://github.com/heuermh))
- [ADAM-1693] Add adam-shell friendly VariantContextRDD.saveAsVcf method. [\#1696](https://github.com/bigdatagenomics/adam/pull/1696) ([heuermh](https://github.com/heuermh))
- [ADAM-1688] Add bdg-formats exclusion to org.hammerlab:genomic-loci dependency. [\#1690](https://github.com/bigdatagenomics/adam/pull/1690) ([heuermh](https://github.com/heuermh))
- [ADAM-1679] Unmapped items should not get caught in requirement when sorting [\#1687](https://github.com/bigdatagenomics/adam/pull/1687) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1566] Merge VCF header lines with VCFHeaderLineCount.INTEGER correctly. [\#1685](https://github.com/bigdatagenomics/adam/pull/1685) ([heuermh](https://github.com/heuermh))
- [ADAM-1682] Add variant quality field. [\#1684](https://github.com/bigdatagenomics/adam/pull/1684) ([fnothaft](https://github.com/fnothaft))
- Remove adam- prefix from module directory names. [\#1681](https://github.com/bigdatagenomics/adam/pull/1681) ([heuermh](https://github.com/heuermh))
- Update to hadoop-bam 7.9.0 and htsjdk 2.11.0. [\#1678](https://github.com/bigdatagenomics/adam/pull/1678) ([heuermh](https://github.com/heuermh))
- [ADAM-1676] Add more finely grained validation for INFO/FORMAT fields. [\#1677](https://github.com/bigdatagenomics/adam/pull/1677) ([fnothaft](https://github.com/fnothaft))
- Python API fixes for AlignmentRecordRDD [\#1675](https://github.com/bigdatagenomics/adam/pull/1675) ([akmorrow13](https://github.com/akmorrow13))
- [ADAM-1673] Don't set PL to empty when no PL is attached to a gVCF record [\#1674](https://github.com/bigdatagenomics/adam/pull/1674) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1670] Add ability to selectively project VCF fields. [\#1671](https://github.com/bigdatagenomics/adam/pull/1671) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1663] Enable read groups with repeated names when unioning. [\#1665](https://github.com/bigdatagenomics/adam/pull/1665) ([fnothaft](https://github.com/fnothaft))
- Maint 2.11 0.18.0 [\#1659](https://github.com/bigdatagenomics/adam/pull/1659) ([Douglas-H](https://github.com/Douglas-H))
- [ADAM-1630] Overhauled docs introduction and added architecture section. [\#1653](https://github.com/bigdatagenomics/adam/pull/1653) ([fnothaft](https://github.com/fnothaft))
- Add adamR script [\#1651](https://github.com/bigdatagenomics/adam/pull/1651) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1647] Fix bad JAR discovery grep in bin/pyadam. [\#1648](https://github.com/bigdatagenomics/adam/pull/1648) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1548] Generate reStructuredText from pandoc markdown. [\#1646](https://github.com/bigdatagenomics/adam/pull/1646) ([fnothaft](https://github.com/fnothaft))
- Algorithms docs formatting [\#1645](https://github.com/bigdatagenomics/adam/pull/1645) ([gunjanbaid](https://github.com/gunjanbaid))
- Cleaned up docs. [\#1642](https://github.com/bigdatagenomics/adam/pull/1642) ([gunjanbaid](https://github.com/gunjanbaid))
- Making example code compatible with current ADAM build [\#1641](https://github.com/bigdatagenomics/adam/pull/1641) ([devin-petersohn](https://github.com/devin-petersohn))
- Cleaning up formatting and spacing of docs. [\#1640](https://github.com/bigdatagenomics/adam/pull/1640) ([devin-petersohn](https://github.com/devin-petersohn))
- added ExtractRegions [\#1637](https://github.com/bigdatagenomics/adam/pull/1637) ([antonkulaga](https://github.com/antonkulaga))
- [ADAM-1635] Eliminate passing FASTQ splittable status via config. [\#1636](https://github.com/bigdatagenomics/adam/pull/1636) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1614] Add VariantContextRDD to R and Python APIs. [\#1628](https://github.com/bigdatagenomics/adam/pull/1628) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1615] Add transform and transmute APIs to Java, R, and Python [\#1627](https://github.com/bigdatagenomics/adam/pull/1627) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1625] Use explicit types for header lines [\#1626](https://github.com/bigdatagenomics/adam/pull/1626) ([heuermh](https://github.com/heuermh))
- [ADAM-1623] Add ProcessingStep to adam-codegen. [\#1624](https://github.com/bigdatagenomics/adam/pull/1624) ([heuermh](https://github.com/heuermh))
- [ADAM-1607] Update distribution assembly task to attach assembly überjar [\#1622](https://github.com/bigdatagenomics/adam/pull/1622) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1490] Add asSingleFile to saveAsFastq and related. [\#1621](https://github.com/bigdatagenomics/adam/pull/1621) ([heuermh](https://github.com/heuermh))
- Update load method docs in Python and R. [\#1619](https://github.com/bigdatagenomics/adam/pull/1619) ([heuermh](https://github.com/heuermh))
- [ADAM-1616] Resolve installation directory if scripts are symlinks. [\#1617](https://github.com/bigdatagenomics/adam/pull/1617) ([heuermh](https://github.com/heuermh))
- [ADAM-1611] Extend pipe APIs to Java, Python, and R. [\#1613](https://github.com/bigdatagenomics/adam/pull/1613) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1610] Mark non-serializable field in TwoBitFile as transient. [\#1612](https://github.com/bigdatagenomics/adam/pull/1612) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1554] Support saving BGZF VCF output. [\#1608](https://github.com/bigdatagenomics/adam/pull/1608) ([fnothaft](https://github.com/fnothaft))
- Adding examples of how to use joins in the real world [\#1605](https://github.com/bigdatagenomics/adam/pull/1605) ([devin-petersohn](https://github.com/devin-petersohn))
- [ADAM-1599] Add explicit functions for updating GenomicRDD metadata. [\#1600](https://github.com/bigdatagenomics/adam/pull/1600) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1576] Allow translation between two different GenomicRDD types. [\#1598](https://github.com/bigdatagenomics/adam/pull/1598) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1444] Ignore failed push to Coveralls. [\#1595](https://github.com/bigdatagenomics/adam/pull/1595) ([fnothaft](https://github.com/fnothaft))
- Testing, testing, 1... 2... 3... [\#1592](https://github.com/bigdatagenomics/adam/pull/1592) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1417] Removed unused Projection.apply method, add test for Filter. [\#1591](https://github.com/bigdatagenomics/adam/pull/1591) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1579] Add unit test coverage for BED12 format. [\#1587](https://github.com/bigdatagenomics/adam/pull/1587) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1585] Support additional Illumina FASTQ metadata. [\#1586](https://github.com/bigdatagenomics/adam/pull/1586) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1438] Add ability to save FASTA back as a single file. [\#1581](https://github.com/bigdatagenomics/adam/pull/1581) ([fnothaft](https://github.com/fnothaft))
- Bump bdg-formats correctly to 0.11.1, not SNAPSHOT. [\#1577](https://github.com/bigdatagenomics/adam/pull/1577) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1573] Remove unused Unaligned trait. [\#1574](https://github.com/bigdatagenomics/adam/pull/1574) ([fnothaft](https://github.com/fnothaft))
- Slurm deployment readme [\#1571](https://github.com/bigdatagenomics/adam/pull/1571) ([jpdna](https://github.com/jpdna))
- [ADAM-1564] Read VCF header from stream in VCFOutFormatter. [\#1565](https://github.com/bigdatagenomics/adam/pull/1565) ([heuermh](https://github.com/heuermh))
- [ADAM-1562] Index off by one for VCF genotype Number=A attributes. [\#1563](https://github.com/bigdatagenomics/adam/pull/1563) ([heuermh](https://github.com/heuermh))
- [ADAM-1533] Set Theory [\#1561](https://github.com/bigdatagenomics/adam/pull/1561) ([devin-petersohn](https://github.com/devin-petersohn))
- Freebayes FORMAT=<ID=AO,Number=A attribute throws ArrayIndexOutOfBoundsException [\#1560](https://github.com/bigdatagenomics/adam/pull/1560) ([heuermh](https://github.com/heuermh))
- [ADAM-1551] Emit non-reference model genotype at called sites. [\#1559](https://github.com/bigdatagenomics/adam/pull/1559) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1449] Add loadSequenceDictionary to ADAM context. [\#1557](https://github.com/bigdatagenomics/adam/pull/1557) ([heuermh](https://github.com/heuermh))
- [ADAM-1537] Rename o.b.adam.apis.java package to o.b.adam.api.java [\#1556](https://github.com/bigdatagenomics/adam/pull/1556) ([heuermh](https://github.com/heuermh))
- [ADAM-1549] Make regions provided to filterByOverlappingRegions an Iterable. [\#1550](https://github.com/bigdatagenomics/adam/pull/1550) ([fnothaft](https://github.com/fnothaft))
- [ADAM-941] Automatically generate projection enums. [\#1547](https://github.com/bigdatagenomics/adam/pull/1547) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1361] Fix misnamed ADAM überjar. [\#1546](https://github.com/bigdatagenomics/adam/pull/1546) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1257] Add program record support for alignment/fragment files. [\#1545](https://github.com/bigdatagenomics/adam/pull/1545) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1359] Merge `reads2fragments` and `fragments2reads` into `transformFragments` [\#1543](https://github.com/bigdatagenomics/adam/pull/1543) ([fnothaft](https://github.com/fnothaft))
- Fix minor format mistakes (and typo) in docs [\#1542](https://github.com/bigdatagenomics/adam/pull/1542) ([kkaneda](https://github.com/kkaneda))
- Add a simple unit test to SingleFastqInputFormat [\#1541](https://github.com/bigdatagenomics/adam/pull/1541) ([kkaneda](https://github.com/kkaneda))
- Support locus predicate in Transform [\#1540](https://github.com/bigdatagenomics/adam/pull/1540) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1421] Add java API for `loadReferenceFile`. [\#1536](https://github.com/bigdatagenomics/adam/pull/1536) ([fnothaft](https://github.com/fnothaft))
- Refactor Vcf2ADAM and ADAM2Vcf into TransformGenotypes and TransformVariants [\#1532](https://github.com/bigdatagenomics/adam/pull/1532) ([heuermh](https://github.com/heuermh))
- [ADAM-1530] Support loading GO:query (S/CR/B)AMs as fragments. [\#1531](https://github.com/bigdatagenomics/adam/pull/1531) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1169] Write GFF header line pragma in single file mode. [\#1529](https://github.com/bigdatagenomics/adam/pull/1529) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1501] Compute coverage using Dataset API. [\#1528](https://github.com/bigdatagenomics/adam/pull/1528) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1497] Add union to GenomicRDD. [\#1526](https://github.com/bigdatagenomics/adam/pull/1526) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1486] Respect validation stringency if BAM header load fails. [\#1525](https://github.com/bigdatagenomics/adam/pull/1525) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1499] Enable reuse of broadcasted objects in region join. [\#1524](https://github.com/bigdatagenomics/adam/pull/1524) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1520] Bump to bdg-formats 0.11.0. [\#1523](https://github.com/bigdatagenomics/adam/pull/1523) ([fnothaft](https://github.com/fnothaft))
- Adding fragment InFormatter for Bowtie tab5 format [\#1522](https://github.com/bigdatagenomics/adam/pull/1522) ([heuermh](https://github.com/heuermh))
- [ADAM-1328] Rename `Transform` to `TransformAlignments`. [\#1521](https://github.com/bigdatagenomics/adam/pull/1521) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1517] Move to Parquet 1.8.2 in preparation for moving to Spark 2.2.0 [\#1518](https://github.com/bigdatagenomics/adam/pull/1518) ([fnothaft](https://github.com/fnothaft))
- Fixed minor typos in README. [\#1516](https://github.com/bigdatagenomics/adam/pull/1516) ([gunjanbaid](https://github.com/gunjanbaid))
- Making TreeRegionJoin consistent with ShuffleRegionJoin [\#1515](https://github.com/bigdatagenomics/adam/pull/1515) ([devin-petersohn](https://github.com/devin-petersohn))
- Resolve #1508, #1509 for Pipe API [\#1511](https://github.com/bigdatagenomics/adam/pull/1511) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1502] Preserve contig ordering in TwoBitFile sequence dictionary. [\#1508](https://github.com/bigdatagenomics/adam/pull/1508) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1483] Remove collapse parameter from AlignmentRecordRDD.toCoverage [\#1493](https://github.com/bigdatagenomics/adam/pull/1493) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1377] Adding fragment InFormatter for Bowtie tab6 format [\#1491](https://github.com/bigdatagenomics/adam/pull/1491) ([heuermh](https://github.com/heuermh))
- [ADAM-1488] Only increment BQSR min quality by 33 once. [\#1489](https://github.com/bigdatagenomics/adam/pull/1489) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1481] Refactor ADAMContext loadXxx methods for consistency [\#1487](https://github.com/bigdatagenomics/adam/pull/1487) ([heuermh](https://github.com/heuermh))
- Add quality score binner [\#1485](https://github.com/bigdatagenomics/adam/pull/1485) ([fnothaft](https://github.com/fnothaft))
- Clean up ReferenceRegion.scala and add thresholded overlap and covers [\#1484](https://github.com/bigdatagenomics/adam/pull/1484) ([devin-petersohn](https://github.com/devin-petersohn))
- [ADAM-1456] Remove .{type}.adam file extension conversions in type-guessing methods. [\#1482](https://github.com/bigdatagenomics/adam/pull/1482) ([heuermh](https://github.com/heuermh))
- [ADAM-1480] Add switch to disable the fast concat method. [\#1479](https://github.com/bigdatagenomics/adam/pull/1479) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1476] Treat `.` ALT allele as symbolic non-ref. [\#1477](https://github.com/bigdatagenomics/adam/pull/1477) ([fnothaft](https://github.com/fnothaft))
- Adding require for Coverage Conversion and related tests [\#1472](https://github.com/bigdatagenomics/adam/pull/1472) ([devin-petersohn](https://github.com/devin-petersohn))
- Add cache argument to loadFeatures, additional Feature timers [\#1427](https://github.com/bigdatagenomics/adam/pull/1427) ([heuermh](https://github.com/heuermh))
- [ADAM-882] R API [\#1397](https://github.com/bigdatagenomics/adam/pull/1397) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1018] Add support for Spark SQL Datasets. [\#1391](https://github.com/bigdatagenomics/adam/pull/1391) ([fnothaft](https://github.com/fnothaft))
- WIP Python API [\#1387](https://github.com/bigdatagenomics/adam/pull/1387) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1365] Apply validation stringency to reads on missing contigs when MD tagging [\#1366](https://github.com/bigdatagenomics/adam/pull/1366) ([fnothaft](https://github.com/fnothaft))
- Update dependency and plugin versions [\#1360](https://github.com/bigdatagenomics/adam/pull/1360) ([heuermh](https://github.com/heuermh))
- [ADAM-1330] Move to Spark 2.1.0. [\#1332](https://github.com/bigdatagenomics/adam/pull/1332) ([fnothaft](https://github.com/fnothaft))
- Efficient Joins and (re)Partitioning [\#1324](https://github.com/bigdatagenomics/adam/pull/1324) ([devin-petersohn](https://github.com/devin-petersohn))
### Version 0.22.0 ###
**Closed issues:**
- Realign all reads at target site, not just reads with no mismatches [\#1469](https://github.com/bigdatagenomics/adam/issues/1469)
- Parallel file merger fails if the output file is smaller than the HDFS block size [\#1467](https://github.com/bigdatagenomics/adam/issues/1467)
- Add new realigner arguments to docs [\#1465](https://github.com/bigdatagenomics/adam/issues/1465)
- Recalibrate method misspelled as recalibateBaseQualities [\#1463](https://github.com/bigdatagenomics/adam/issues/1463)
- FASTQ may try to split GZIPed files [\#1459](https://github.com/bigdatagenomics/adam/issues/1459)
- Update to Hadoop-BAM 7.8.0 [\#1455](https://github.com/bigdatagenomics/adam/issues/1455)
- Publish Markdown and Scaladoc to the interwebs [\#1453](https://github.com/bigdatagenomics/adam/issues/1453)
- Make VariantContextConverter public [\#1451](https://github.com/bigdatagenomics/adam/issues/1451)
- Apply method in FragmentRDD is package private [\#1445](https://github.com/bigdatagenomics/adam/issues/1445)
- Thread pool will block inside of pipe command for streams too large to buffer [\#1442](https://github.com/bigdatagenomics/adam/issues/1442)
- FeatureRDD.apply() does not allow addition of other parameters with defaults in the case class [\#1439](https://github.com/bigdatagenomics/adam/issues/1439)
- Question : Why the number of paired sequence in adam-0.21.0 less than adam-0.19.0? [\#1424](https://github.com/bigdatagenomics/adam/issues/1424)
- loadCoverage missing from Java API [\#1420](https://github.com/bigdatagenomics/adam/issues/1420)
- Estimate contig lengths in SequenceDictionary for BED, GFF3, GTF, and NarrowPeak feature formats [\#1410](https://github.com/bigdatagenomics/adam/issues/1410)
- loadIntervalList FeatureRDD has empty SequenceDictionary [\#1409](https://github.com/bigdatagenomics/adam/issues/1409)
- problem using transform command [\#1406](https://github.com/bigdatagenomics/adam/issues/1406)
- Add coveralls [\#1403](https://github.com/bigdatagenomics/adam/issues/1403)
- INDEL realigner binary search conditional is flipped [\#1402](https://github.com/bigdatagenomics/adam/issues/1402)
- Delete adam-scripts/R [\#1398](https://github.com/bigdatagenomics/adam/issues/1398)
- Data missing when transfroming FASTQ to Adam [\#1393](https://github.com/bigdatagenomics/adam/issues/1393)
- java.io.FileNotFoundException when file exists [\#1385](https://github.com/bigdatagenomics/adam/issues/1385)
- Off-by-1 error in FASTQ InputFormat start positioning code [\#1383](https://github.com/bigdatagenomics/adam/issues/1383)
- Set the wrong value for end for symbolic alts [\#1381](https://github.com/bigdatagenomics/adam/issues/1381)
- RecordGroupDictionary should support `isEmpty` [\#1380](https://github.com/bigdatagenomics/adam/issues/1380)
- Add pipe API in and out formatters for Features [\#1374](https://github.com/bigdatagenomics/adam/issues/1374)
- Increase visibility for SupportedHeaderLines.allHeaderLines [\#1372](https://github.com/bigdatagenomics/adam/issues/1372)
- Bits of VariantContextConverter don't get ValidationStringencied [\#1371](https://github.com/bigdatagenomics/adam/issues/1371)
- Add Markdown docs for Pipe API [\#1368](https://github.com/bigdatagenomics/adam/issues/1368)
- Array[Consensus] not registered [\#1367](https://github.com/bigdatagenomics/adam/issues/1367)
- ValidationStringency in MDTagging should apply to reads on unknown references [\#1365](https://github.com/bigdatagenomics/adam/issues/1365)
- When doing a release, the SNAPSHOT should bump by 0.1.0, not 0.0.1 [\#1364](https://github.com/bigdatagenomics/adam/issues/1364)
- FromKnowns consensus generator fails if no reads overlap a consensus [\#1362](https://github.com/bigdatagenomics/adam/issues/1362)
- Performance tune-up in BQSR [\#1358](https://github.com/bigdatagenomics/adam/issues/1358)
- Increase visibility for ADAMContext.sc and/or getFs... methods [\#1356](https://github.com/bigdatagenomics/adam/issues/1356)
- Pipe API formatters need to be public [\#1354](https://github.com/bigdatagenomics/adam/issues/1354)
- Version 0.21.0: VariantContextConverter fails for 1000G VCF data [\#1353](https://github.com/bigdatagenomics/adam/issues/1353)
- ConsensusModel's can't really be instantiated [\#1352](https://github.com/bigdatagenomics/adam/issues/1352)
- Runtime conflicts in transitive versions of Guava dependency [\#1350](https://github.com/bigdatagenomics/adam/issues/1350)
- Transcript Effects ignored if more than 1 [\#1347](https://github.com/bigdatagenomics/adam/issues/1347)
- Remove "fork" tag from releases [\#1344](https://github.com/bigdatagenomics/adam/issues/1344)
- Refactor isSorted boolean parameters to sorted [\#1341](https://github.com/bigdatagenomics/adam/issues/1341)
- Loading GZipped VCF returns an empty RDD [\#1333](https://github.com/bigdatagenomics/adam/issues/1333)
- Follow up on error messages in build scripts [\#1331](https://github.com/bigdatagenomics/adam/issues/1331)
- Bump Spark 2 build to Spark 2.1.0 [\#1330](https://github.com/bigdatagenomics/adam/issues/1330)
- FeatureRDD instantiation tries to cache the RDD [\#1321](https://github.com/bigdatagenomics/adam/issues/1321)
- Load queryname sorted BAMs as Fragments [\#1303](https://github.com/bigdatagenomics/adam/issues/1303)
- Run Duplicate Marking on Fragments [\#1302](https://github.com/bigdatagenomics/adam/issues/1302)
- GenomicRDD.pipe may hang on failure error codes [\#1282](https://github.com/bigdatagenomics/adam/issues/1282)
- IllegalArgumentException Wrong FS for vcf_head files on HDFS [\#1272](https://github.com/bigdatagenomics/adam/issues/1272)
- java.io.NotSerializableException: org.bdgenomics.formats.avro.AlignmentRecord [\#1240](https://github.com/bigdatagenomics/adam/issues/1240)
- Investigate sorted join in dataset api [\#1223](https://github.com/bigdatagenomics/adam/issues/1223)
- Support looser validation stringency for loading some VCF Integer fields [\#1213](https://github.com/bigdatagenomics/adam/issues/1213)
- Add new feature-overlap command to demonstrate new region joins [\#1194](https://github.com/bigdatagenomics/adam/issues/1194)
- What should our API at the command line look like? [\#1178](https://github.com/bigdatagenomics/adam/issues/1178)
- Split apart partition and join in ShuffleRegionJoin [\#1175](https://github.com/bigdatagenomics/adam/issues/1175)
- Merging files should be multithreaded [\#1164](https://github.com/bigdatagenomics/adam/issues/1164)
- File _rgdict.avro does not exist [\#1150](https://github.com/bigdatagenomics/adam/issues/1150)
- how to collect the .adam files from Spark cluster multiple nodes and some questions about avocado [\#1140](https://github.com/bigdatagenomics/adam/issues/1140)
- JFYI: tiny forked adam-core "0.20.0" release [\#1139](https://github.com/bigdatagenomics/adam/issues/1139)
- Samtools (htslib) integration testing [\#1120](https://github.com/bigdatagenomics/adam/issues/1120)
- AlignmentRecordRDD does not extend GenomicRDD per javac [\#1092](https://github.com/bigdatagenomics/adam/issues/1092)
- Release ADAM version 0.21.0 [\#1088](https://github.com/bigdatagenomics/adam/issues/1088)
- Difference running markdups with and without projection [\#1014](https://github.com/bigdatagenomics/adam/issues/1014)
- ADAM to BAM conversion fails using relative path [\#1012](https://github.com/bigdatagenomics/adam/issues/1012)
- Refactor SequenceDictionary to use Contig instead of SequenceRecord [\#997](https://github.com/bigdatagenomics/adam/issues/997)
- Customize adam-main cli from configuration file [\#918](https://github.com/bigdatagenomics/adam/issues/918)
- genotypeType for genotypes with multiple OtherAlt alleles? [\#897](https://github.com/bigdatagenomics/adam/issues/897)
- How to convert genotype DataFrame to VariantContext DataFrame / RDD [\#886](https://github.com/bigdatagenomics/adam/issues/886)
- Ensure Java API is up-to-date with Scala API [\#855](https://github.com/bigdatagenomics/adam/issues/855)
- Improve parallelism during FASTA output [\#842](https://github.com/bigdatagenomics/adam/issues/842)
- Explicitly validate user args passed to transform enhancement [\#841](https://github.com/bigdatagenomics/adam/issues/841)
- BroadcastRegionJoin fails with unmapped reads [\#821](https://github.com/bigdatagenomics/adam/issues/821)
- Resolve Fragment vs. SingleReadBucket [\#789](https://github.com/bigdatagenomics/adam/issues/789)
- Add profile for skipping test compilation/resolution [\#713](https://github.com/bigdatagenomics/adam/issues/713)
- Next on empty iterator in BroadcastRegionJoin [\#661](https://github.com/bigdatagenomics/adam/issues/661)
- Cleanup code smell in sort work balancing code [\#635](https://github.com/bigdatagenomics/adam/issues/635)
- Remove reliance on MD tags [\#622](https://github.com/bigdatagenomics/adam/issues/622)
- Provide low-impact alternative to `transform -repartition` for reducing partition size [\#594](https://github.com/bigdatagenomics/adam/issues/594)
- Clean up Rich records [\#577](https://github.com/bigdatagenomics/adam/issues/577)
- Create standardized, interpretable exceptions for error reporting [\#420](https://github.com/bigdatagenomics/adam/issues/420)
- Create ADAM Benchmarking suite [\#120](https://github.com/bigdatagenomics/adam/issues/120)
**Merged and closed pull requests:**
- [ADAM-1469] Don't filter on whether reads have mismatches during realignment [\#1470](https://github.com/bigdatagenomics/adam/pull/1470) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1467] Skip `concat` call if there is only one shard. [\#1468](https://github.com/bigdatagenomics/adam/pull/1468) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1465] Updating realigner CLI docs. [\#1466](https://github.com/bigdatagenomics/adam/pull/1466) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1463] Rename recalibateBaseQualities method as recalibrateBaseQualities [\#1464](https://github.com/bigdatagenomics/adam/pull/1464) ([heuermh](https://github.com/heuermh))
- [ADAM-1453] Add hooks to publish ADAM docs from CI flow. [\#1461](https://github.com/bigdatagenomics/adam/pull/1461) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1459] Don't split FASTQ when compressed. [\#1459](https://github.com/bigdatagenomics/adam/pull/1459) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1451] Make VariantContextConverter class and convert methods public [\#1452](https://github.com/bigdatagenomics/adam/pull/1452) ([fnothaft](https://github.com/fnothaft))
- Moving API overview from building apps doc to new source file. [\#1450](https://github.com/bigdatagenomics/adam/pull/1450) ([heuermh](https://github.com/heuermh))
- [ADAM-1424] Adding test for reads dropped in 0.21.0. [\#1448](https://github.com/bigdatagenomics/adam/pull/1448) ([heuermh](https://github.com/heuermh))
- [ADAM-1439] Add inferSequenceDictionary ctr to FeatureRDD. [\#1447](https://github.com/bigdatagenomics/adam/pull/1447) ([heuermh](https://github.com/heuermh))
- [ADAM-1445] Make apply method for FragmentRDD public. [\#1446](https://github.com/bigdatagenomics/adam/pull/1446) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1442] Fix thread pool deadlock in GenomicRDD.pipe [\#1443](https://github.com/bigdatagenomics/adam/pull/1443) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1164] Add parallel file merger. [\#1441](https://github.com/bigdatagenomics/adam/pull/1441) ([fnothaft](https://github.com/fnothaft))
- Dependency version bump + BroadcastRegionJoin fix [\#1440](https://github.com/bigdatagenomics/adam/pull/1440) ([fnothaft](https://github.com/fnothaft))
- added JavaApi for loadCoverage [\#1437](https://github.com/bigdatagenomics/adam/pull/1437) ([akmorrow13](https://github.com/akmorrow13))
- Update versions, etc. in build docs [\#1435](https://github.com/bigdatagenomics/adam/pull/1435) ([heuermh](https://github.com/heuermh))
- Add test sample(verify number of reads in loadAlignments function) and ADAM SNAPSHOT document [\#1433](https://github.com/bigdatagenomics/adam/pull/1433) ([xubo245](https://github.com/xubo245))
- Add cache argument to loadFeatures, additional Feature timers [\#1427](https://github.com/bigdatagenomics/adam/pull/1427) ([heuermh](https://github.com/heuermh))
- feat: speed up 2bit file extract [\#1426](https://github.com/bigdatagenomics/adam/pull/1426) ([Blaok](https://github.com/Blaok))
- BQSR refactor for perf improvements [\#1423](https://github.com/bigdatagenomics/adam/pull/1423) ([fnothaft](https://github.com/fnothaft))
- Add ADAMContext/GenomicRDD/pipe docs [\#1422](https://github.com/bigdatagenomics/adam/pull/1422) ([fnothaft](https://github.com/fnothaft))
- INDEL realigner cleanup [\#1412](https://github.com/bigdatagenomics/adam/pull/1412) ([fnothaft](https://github.com/fnothaft))
- Estimate contig lengths in SequenceDictionary for BED, GFF3, GTF, and NarrowPeak feature formats [\#1411](https://github.com/bigdatagenomics/adam/pull/1411) ([heuermh](https://github.com/heuermh))
- Add coveralls badge to README.md. [\#1408](https://github.com/bigdatagenomics/adam/pull/1408) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1403] Push coverage reports to Coveralls. [\#1404](https://github.com/bigdatagenomics/adam/pull/1404) ([fnothaft](https://github.com/fnothaft))
- Added instrumentation timers around joins. [\#1401](https://github.com/bigdatagenomics/adam/pull/1401) ([fnothaft](https://github.com/fnothaft))
- Add Apache Spark version to --version text [\#1400](https://github.com/bigdatagenomics/adam/pull/1400) ([heuermh](https://github.com/heuermh))
- [ADAM-1398] Delete adam-scripts/R. [\#1399](https://github.com/bigdatagenomics/adam/pull/1399) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1383] Use gt instead of gteq in FASTQ input format line size checks [\#1396](https://github.com/bigdatagenomics/adam/pull/1396) ([fnothaft](https://github.com/fnothaft))
- Maint spark2 2.11 0.21.0 [\#1395](https://github.com/bigdatagenomics/adam/pull/1395) ([A-Tsai](https://github.com/A-Tsai))
- [ADAM-1393] fix missing reads when transforming fastq to adam [\#1394](https://github.com/bigdatagenomics/adam/pull/1394) ([A-Tsai](https://github.com/A-Tsai))
- [ADAM-1380] Adds isEmpty method to RecordGroupDictionary. [\#1392](https://github.com/bigdatagenomics/adam/pull/1392) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1381] Fix Variant end position. [\#1389](https://github.com/bigdatagenomics/adam/pull/1389) ([fnothaft](https://github.com/fnothaft))
- Make javac see that AlignmentRecordRDD extends GenomicRDD [\#1386](https://github.com/bigdatagenomics/adam/pull/1386) ([fnothaft](https://github.com/fnothaft))
- Added ShuffleRegionJoin usage docs [\#1384](https://github.com/bigdatagenomics/adam/pull/1384) ([devin-petersohn](https://github.com/devin-petersohn))
- Misc. INDEL realigner bugfixes [\#1382](https://github.com/bigdatagenomics/adam/pull/1382) ([fnothaft](https://github.com/fnothaft))
- Add pipe API in and out formatters for Features [\#1378](https://github.com/bigdatagenomics/adam/pull/1378) ([heuermh](https://github.com/heuermh))
- [ADAM-1356] Make ADAMContext.getFsAndFiles and related protected visibility [\#1376](https://github.com/bigdatagenomics/adam/pull/1376) ([heuermh](https://github.com/heuermh))
- [ADAM-1372] Increase visibility for DefaultHeaderLines.allHeaderLines [\#1375](https://github.com/bigdatagenomics/adam/pull/1375) ([heuermh](https://github.com/heuermh))
- [ADAM-1371] Wrap ADAM->htsjdk VariantContext conversion with validation stringency. [\#1373](https://github.com/bigdatagenomics/adam/pull/1373) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1367] Register Consensus array for serialization. [\#1369](https://github.com/bigdatagenomics/adam/pull/1369) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1365] Apply validation stringency to reads on missing contigs when MD tagging [\#1366](https://github.com/bigdatagenomics/adam/pull/1366) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1362] Fixing issue where FromKnowns consensus model fails if no reads hit a target. [\#1363](https://github.com/bigdatagenomics/adam/pull/1363) ([fnothaft](https://github.com/fnothaft))
- [ADAM-1352] Clean up consensus model usage. [\#1357](https://github.com/bigdatagenomics/adam/pull/1357) ([fnothaft](https://github.com/fnothaft))
- Increase visibility for InFormatter case classes from package private to public [\#1355](https://github.com/bigdatagenomics/adam/pull/1355) ([heuermh](https://github.com/heuermh))
- Use htsjdk getAttributeAsList for VCF INFO ANN key [\#1348](https://github.com/bigdatagenomics/adam/pull/1348) ([heuermh](https://github.com/heuermh))
- Fixes parsing variant annotations for multi-allelic rows [\#1346](https://github.com/bigdatagenomics/adam/pull/1346) ([majkiw](https://github.com/majkiw))
- Sort pull requests by id [\#1345](https://github.com/bigdatagenomics/adam/pull/1345) ([heuermh](https://github.com/heuermh))
- HBase genotypes backend -revised [\#1335](https://github.com/bigdatagenomics/adam/pull/1335) ([jpdna](https://github.com/jpdna))
- [ADAM-1330] Move to Spark 2.1.0. [\#1332](https://github.com/bigdatagenomics/adam/pull/1332) ([fnothaft](https://github.com/fnothaft))
- Support deduping fragments [\#1309](https://github.com/bigdatagenomics/adam/pull/1309) ([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))
- Added test to try and repro #1282. [\#1292](https://github.com/bigdatagenomics/adam/pull/1292) ([fnothaft](https://github.com/fnothaft))
### 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)