- ISSUE 264: Parquet-related Utility Classes
- ISSUE 259: ADAMFlatGenotype is a smaller, flat version of a genotype schema
- ISSUE 266: Removed extra command 'BuildInformation'
- ISSUE 263: Added AdamContext.referenceLengthFromCigar
- ISSUE 260: Modifying conversion code to resolve #112.
- ISSUE 258: Adding an 'args' parameter to the plugin framework.
- ISSUE 262: Adding reference assembly name to ADAMContig.
- ISSUE 256: Upgrading to Spark 1.0
- ISSUE 257: Adds toString method for sequence dictionary.
- ISSUE 255: Add equals, canEqual, and hashCode methods to MdTag class
- ISSUE 254: Cleanup import statements
- ISSUE 250: Adding ADAM to SAM conversion.
- ISSUE 248: Adding utilities for read trimming.
- ISSUE 252: Added a note about rebasing-off-master to CONTRIBUTING.md
- ISSUE 249: Cosmetic changes to FastaConverter and FastaConverterSuite.
- ISSUE 251: CHANGES.md is updated at release instead of per pull request
- ISSUE 247: For #244, Fragments were incorrect order and incomplete
- ISSUE 246: Making sample ID field in genotype nullable.
- ISSUE 245: Adding ADAMContig back to ADAMVariant.
- ISSUE 243: Rebase PR#238 onto master
- ISSUE 242: Upgrade to Parquet 1.4.3
- ISSUE 241: Fixes to FASTA code to properly handle indices.
- ISSUE 239: Make ADAMVCFOutputFormat public
- ISSUE 233: Build up reference information during cigar processing
- ISSUE 234: Predicate to filter conversion
- ISSUE 235: Remove unused contiglength field
- ISSUE 232: Add
-prettyand-oto theprintcommand - ISSUE 230: Remove duplicate mdtag field
- ISSUE 231: Helper scripts to run an ADAM Console.
- ISSUE 226: Fix ReferenceRegion from ADAMRecord
- ISSUE 225: Change Some to Option to check for unmapped reads
- ISSUE 223: Use SparkConf object to configure SparkContext
- ISSUE 217: Stop using reference IDs and use reference names instead
- ISSUE 220: Update SAM to ADAM conversion
- ISSUE 213: BQSR updates
- ISSUE 214: Upgrade to Spark 0.9.1
- ISSUE 211: FastaConverter Refactor
- ISSUE 212: Cleanup build warnings
- ISSUE 210: Remove Scalariform from process-sources phase
- ISSUE 209: Fix Scalariform issues and Maven warnings
- ISSUE 207: Change from deprecated manifest erasure to runtimeClass
- ISSUE 206: Add Scalariform settings to pom
- ISSUE 204: Update Avro code gen to not mark fields as deprecated.
- ISSUE 203: Move package from edu.berkeley.cs.amplab to org.bdgenomics
- ISSUE 199: Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators
- ISSUE 191: Add repartition parameter
- ISSUE 183: Fixing Job.getInstance call that breaks hadoop 1 compatibility.
- ISSUE 192: Add docs and scripts for creating a release
- ISSUE 193: Issue #137, clarify role of CHANGES.{md,txt}
- ISSUE 187: Add summarize_genotypes command
- ISSUE 178: Upgraded to Hadoop-BAM 0.6.2/Picard 1.107.
- ISSUE 173: Parse annotations out of vcf files
- ISSUE 162: Refactored SequenceDictionary
- ISSUE 180: BQSR using vcf loader
- ISSUE 179: Update maven-surefire-plugin dependency version to 2.17, also create an ...
- ISSUE 175: VariantContext converter refactor
- ISSUE 169: Cleaning up mpileup command
- ISSUE 170: Adding variant field enumerations
- ISSUE 166: Pair-wise genotype concordance of genotype RDDs, with CLI tool
- ISSUE 171: Add back in allele dosage for genotypes.
- ISSUE 167: Fix for Hadoop 1.0.x support
- ISSUE 165: call PluginExecutor in apply method, fixes issue 164
- ISSUE 160: Refactoring FASTA work to break contig sizes.
- ISSUE 78: Upgrade to Spark 0.9 and Scala 2.10
- ISSUE 138: Display Git commit info on command line
- ISSUE 161: Added switches to spark context creation code
- ISSUE 117: Add a "range join" method.
- ISSUE 151: Vcf work concordance and genotype
- ISSUE 150: Remaining variant changes for adam2vcf, unit tests, and CLI modifications
- ISSUE 147: Resurrect VCF conversion code
- ISSUE 148: Moving createSparkContext into core
- ISSUE 142: Enforce Maven and Java versions
- ISSUE 144: Merge of last few days of work on master into this branch
- ISSUE 124: Vcf work rdd master merge
- ISSUE 143: Changing package declaration to match test file location and removing un...
- ISSUE 140: Update README.md
- ISSUE 139: Update README.md
- ISSUE 129: Modified pileup transforms to improve performance + to add options
- ISSUE 116: add fastq interleaver script
- ISSUE 125: Add design doc to CONTRIBUTING document
- ISSUE 114: Changes to RDD utility files for new variant schema
- ISSUE 122: Add IRC Channel to readme
- ISSUE 100: CLI component changes for new variant schema
- ISSUE 108: Adding new PluginExecutor command
- ISSUE 98: Vcf work remove old variant
- ISSUE 104: Added the port erasure to SparkFunSuite's cleanup.
- ISSUE 107: Cleaning up change documentation.
- ISSUE 99: Encoding tag types in the ADAMRecord attributes, adding the 'tags' command
- ISSUE 105: Add initial documentation on contributing
- ISSUE 97: New schema, variant context converter changes, and removal of old genoty...
- ISSUE 79: Adding ability to convert reference FASTA files for nucleotide sequences
- ISSUE 91: Minor change, increase adam-cli usage width to 150 characters
- ISSUE 86: Fixes to pileup code
- ISSUE 88: Added function for building variant context from genotypes.
- ISSUE 81: Update README and cleanup top-level cli help text
- ISSUE 76: Changing hadoop fs call to be compatible with Hadoop 1.
- ISSUE 74: Updated CHANGES.txt to include note about the recursive-load branch.
- ISSUE 73: Support for loading/combining multiple ADAM files into a single RDD.
- ISSUE 72: Added ability to create regions from reads, and to merge adjacent regions
- ISSUE 71: Change RecalTable to use optimized phred calculations
- ISSUE 68: sonatype-nexus-snapshots repository is already in parent oss-parent-7 pom
- ISSUE 67: fix for wildcard exclusion maven warnings
- ISSUE 65: Create a cache for phred -> double values instead of recalculating
- ISSUE 60: Bugfix for BQSR: Offset into qualityScore list was wrong
- ISSUE 66: add pluginDependency section and remove versions in plugin sections
- ISSUE 61: Filter utility for inverse of Projection
- ISSUE 48: Fix read groups mapping and add Y as base type
- ISSUE 36: Adding reads to rods transformation.
- ISSUE 56: Adding Yy as base in MdTag
- ISSUE 53: Fix Hadoop 2.2.0 support, upgrade to Spark 0.8.1
- ISSUE 52: Attributes: Use 't' instead of ',', as , is a valid character
- ISSUE 47: Adding containsRefName to SequenceDictionary
- ISSUE 46: Reduce logging for the actual adamSave job
- ISSUE 45: Make MdTag immutable
- ISSUE 38: Small bugfixes and cleanups to BQSR
- ISSUE 40: Fixing reference position from offset implementation
- ISSUE 31: Fixing a few issues in the ADAM2VCF2ADAM pipeline.
- ISSUE 30: Suppress parquet logging in FieldEnumerationSuite
- ISSUE 28: Fix build warnings
- ISSUE 24: Add unit tests for marking duplicates
- ISSUE 26: Fix unmapped reads in sequence dictionary
- ISSUE 23: Generalizing the Projection class
- ISSUE 25: Adding support for before, after clauses to SparkFunSuite.
- ISSUE 22: Add a unit test for sorting reads
- ISSUE 21: Adding rod functionality: a specialized grouping of pileup data.
- ISSUE 13: Cleaning up VCF<->ADAM pipeline
- ISSUE 20: Added Apache License 2.0 boilerplate to tops of all the GB-(c) files
- ISSUE 19: Allow the Hadoop version to be specified
- ISSUE 17: Fix transform -sort_reads partitioning. Add -coalesce option to transform.
- ISSUE 16: Fixing an issue in pileup generation and in the MdTag util.
- ISSUE 15: Tweaks 1
- ISSUE 12: Subclass testing bug in AdamContext.adamLoad
- ISSUE 11: Missing brackets in VcfConverter.getType
- ISSUE 10: Moved record field name enum over to the projections package.
- ISSUE 8: Fixes to sorting in ReferencePosition
- ISSUE 4: New SparkFunSuite test support class, logging util and new BQSR test.
- ISSUE 1: Fix scalatest configuration and fix unit tests
- ISSUE 14: Converting some of the Option() calls to Some()
- ISSUE 13: Cleaning up VCF<->ADAM pipeline
- ISSUE 9: Adding support for a Sequence Dictionary from BAM files
- ISSUE 8: Fixes to sorting in ReferencePosition
- ISSUE 7: ADAM variant and genotype formats; and a VCF->ADAM converter
- ISSUE 4: New SparkFunSuite test support class, logging util and new BQSR test.
- ISSUE 3: Adding in implicit conversion functions for going between Java and Scala...
- ISSUE 2: Update from Spark 0.7.3 to 0.8.0-incubating
- ISSUE 1: Fix scalatest configuration and fix unit tests