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ADAM 0.13.0 Released

ADAM 0.13.0 is now available!

This release includes genome visualization to view aligned reads and coverage information over a reference region. You simply run e.g. adam viz myreads.adam chr1 from the ADAM source directory and open your favorite web browser to http://localhost:8080/ to view your data.

This release also includes a number of features and bug fixes including upgrading to Spark 1.0.1.

  • ISSUE 343: Allow retrying on failure for HTTPRangedByteAccess
  • ISSUE 349: Fix for a NullPointerException when hostname is null in Task Metrics
  • ISSUE 347: Bug fix for genome browser
  • ISSUE 346: Genome visualization
  • ISSUE 342: [ADAM-309] Update to bdg-formats 0.2.0
  • ISSUE 333: [ADAM-332] Upgrades ADAM to Spark 1.0.1.
  • ISSUE 341: [ADAM-340] Adding the TrackedLayout trait and implementation.
  • ISSUE 337: [ADAM-335] Updated README.md to reflect migration to appassembler.
  • ISSUE 311: Adding several simple normalizations.
  • ISSUE 330: Make mismatch and deletes positions accessible
  • ISSUE 334: Moving code coverage into a profile
  • ISSUE 329: Add count of mismatches to mdtag
  • ISSUE 328: [ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.
  • ISSUE 325: Adding documentation for commit/issue nomenclature and rebasing

This summer, we also quietly pushed out a 0.12.1 release that included a number of features (e.g. Parquet and indexed Parquet Spark RDDs, k-mer/q-mer counting, fixed depth prefix tries) and bug fixes:

  • ISSUE 308: Fixing the ‘index 0’ bug in features2adam
  • ISSUE 306: Adding code for lifting over between sequences and the reference genome.
  • ISSUE 320: Remove extraneous implicit methods in ReferenceMappingContext
  • ISSUE 314: Updates to indel realigner to improve performance and accuracy.
  • ISSUE 319: Adding scripts for publishing scaladoc.
  • ISSUE 315: Added table of (wall-clock) stage durations when print_metrics is used
  • ISSUE 312: Fixing sources jar
  • ISSUE 313: Making the CredentialsProperties file optional
  • ISSUE 267: Parquet and indexed Parquet RDD implementations, and indices.
  • ISSUE 301: Add Beacon’s AlleleCount
  • ISSUE 293: Add aggregation and display of metrics obtained from Spark
  • ISSUE 295: Fix broken link to ADAM specification for storing reads.
  • ISSUE 292: Cleaning up scaladoc generation warnings.
  • ISSUE 289: Modifying interleaved fastq format to be hadoop version independent.
  • ISSUE 288: Add ADAMFeature to Kryo registrator
  • ISSUE 286: Removing some debug printout that was left in.
  • ISSUE 287: Cleaning hadoop dependencies
  • ISSUE 285: Refactoring read groups to increase the amount of data stored.
  • ISSUE 284: Cleaning up build warnings.
  • ISSUE 280: Move to bdg-formats
  • ISSUE 283: Fix reference name comment
  • ISSUE 282: Minor cleanup on interleaved FASTQ input format.
  • ISSUE 277: Implemented HTTPRangedByteAccess.
  • ISSUE 274: Added clarifying note to ADAMVariantContext
  • ISSUE 279: Simplify format-source
  • ISSUE 278: Use maven license plugin to ensure source has correct license
  • ISSUE 268: Adding fixed depth prefix trie implementation
  • ISSUE 273: Fixes issue in reference models where strings are not sanitized on collection from avro.
  • ISSUE 272: Created command categories
  • ISSUE 269: Adding k-mer and q-mer counting.
  • ISSUE 271: Consolidate Parquet logging configuration

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