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avocado

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  • ISSUE 95: Updating ADAM to 0.12.2-SNAPSHOT with migration to bdg-formats 0.2.0.
  • ISSUE 93: SNAP streaming changes
  • ISSUE 92: Adding a few fixes for running on a cluster.
  • ISSUE 91: Adding fast aligner.
  • ISSUE 90: Updating active region threshold.
  • ISSUE 89: Adding release scripts.
  • ISSUE 88: Removing duplicate write of header.
  • ISSUE 87: Cleaning up avocado build.
  • ISSUE 85: Fixing dependency issues due to injection of javax.servlet.
  • ISSUE 84: Fixing read group code after #285 merged in adam upstream.
  • ISSUE 83: Updating for move over to the bdg-formats repository.
  • ISSUE 82: Fixed IO deadlock when running SNAP as a read frontend.
  • ISSUE 81: Fixing issues with writing BAMs to standard input for external read call
  • ISSUE 80: Changed license header to new BDGenomics license header.
  • ISSUE 78: Fixing build.
  • ISSUE 76: Adding generic stub for external variant callers.
  • ISSUE 77: Refactoring assembler into a general haplotype based caller.
  • ISSUE 75: Upgrade to ADAM 0.10.1-SNAPSHOT stream
  • ISSUE 74: Refactoring transition matrix to allow for cleaner configuration
  • ISSUE 72: Adding code to align reads with SNAP.
  • ISSUE 70: Update config and debug
  • ISSUE 64: Add flanks to gather
  • ISSUE 63: Updated pair haplotype scoring method
  • ISSUE 62: Change locuspredicate to unique read mapped predicate
  • ISSUE 61: Fixes to HMM to add reference padding.
  • ISSUE 60: Remove is methods from variantcall
  • ISSUE 59: Get contig length from adamcontig
  • ISSUE 52: Refactor HMMAligner and add testing for HMMAligner
  • ISSUE 56: Parametrize flanking sequence length for k-mer graph creation
  • ISSUE 55: Simplify haplotype queue creation
  • ISSUE 46: Refactor KmerGraph creation
  • ISSUE 53: Use function from ADAM to create reference sequence
  • ISSUE 51: Update refid to use refname instead
  • ISSUE 50: Parameterize HMM
  • ISSUE 49: Fixes to HMM/Haplotype code to correct indel calling.
  • ISSUE 48: Fix scheme issue with HDFS
  • ISSUE 47: Move haplotype to separate classes
  • ISSUE 45: Change snp caller interface to use rods exclusively
  • ISSUE 44: Homozygous ref and alt were flipped in terms of writing/saving
  • ISSUE 43: Upgrade adam to 0.9.1-SNAPSHOT and Spark to 0.9.1
  • ISSUE 42: Use sequence load instead of only adam load for reference data
  • ISSUE 41: Update Scalariform to be consistent with ADAM
  • ISSUE 40: Move all files to proper package subdirectory
  • ISSUE 38: Updated avocado to move to org.bdgenomics, and to move to ADAM 0.8.1-SNAPSHOT
  • ISSUE 37: Splitting assembler into basic components (HMM, de Brujin graph, etc.)
  • ISSUE 28: Fixes to assembler to get simple SNP calling working.
  • ISSUE 34: Add input stage to sample configs
  • ISSUE 32: Remove ReadModifier.scala, which appears to be dead code.
  • ISSUE 30: Remove lingering references to VariantType, which was removed from ADAM
  • ISSUE 29: Updated variant callers to remove variant type field, as it has been removed in ADAM
  • ISSUE 21: Adding configurable input stage to pipeline.
  • ISSUE 26: Updating to point to ADAM 0.7.2 snapshot release.
  • ISSUE 24: Two changes: Update to build against ADAM 0.7.1-SNAPSHOT
  • ISSUE 23: [WIP] Genotype likelihood calc was flipped
  • ISSUE 22: Build changes for new schema
  • ISSUE 20: Issue #19 Change references from ADAMFastaNucleotideContig to ADAMNucleo...
  • ISSUE 17: Added a filter that filters genotypes that have been called with a high strand bias.
  • ISSUE 18: Reupgraded to Spark 0.9.0. Added config for assembler.
  • ISSUE 16: Reverts upgrade to spark 0.9.0
  • ISSUE 15: Upgraded avocado to spark 0.9.0 and scala 2.10.3.
  • ISSUE 14: Adding indel realigner to pipeline.
  • ISSUE 13: Working pipeline. Added simple first cut configuration file.
  • ISSUE 12: Adding optimized DefaultPartitionSet, better documentation, and tests.
  • ISSUE 11: Adding support in for new FASTA contig class in ADAM.
  • ISSUE 10: Cleanup 0.0.2
  • ISSUE 8: General cleanup to remove cruft from merging code.
  • ISSUE 7: Converting project over to maven.
  • ISSUE 6: Updating with new variant/genotype implementations from Adam PR #13.
  • ISSUE 4: Calling variants from local assembly
  • ISSUE 3: EMforAlleles contains two main methods: emForMAFs and emForAFS.
  • ISSUE 5: Cleaning up with new ADAMRod.
  • ISSUE 2: Adding read filtering.
  • ISSUE 1: Modified to allow VCF input containing MAFs for more advanced calling