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
- 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