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The NCBI NGS Software Development Kit
Contact: sra-tools@ncbi.nlm.nih.gov

NCBI External Developer Release: NGS SDK 1.2.5
July 11, 2016

  blast, kfg, ncbi-vdb, sra-tools, vfs: restored possibility to disable local caching
  htsjdk: Several JVM crashes related to a number of open files were fixed. New property to disable auto-download was integrated into HTSJDK
  kfg: When loading configuration files on Windows USERPROFILE environment variable is used before HOME
  ngs, search, sra-search: sra-search was modified to support multiple threads.
  ngs-engine, ngs-tools, sra-tools, vfs: The "auxiliary" nodes in configuration are now ignored
  ngs-engine: Added support for blob-by-blob access to SEQUENCE table
  ngs-engine: removed a potential memory leak in NGS_CursorMake()
  ngs: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs
  ngs: now supports parallel compilation with "make -j N"
  vfs: environment variable VDB_PWFILE is no longer used


NCBI External Developer Release: NGS SDK 1.2.4
May 25, 2016

  build: MSVS 2013 toolset (12.0) is now supported across all repositories
  doc, ngs: updated javadoc to include throws and other missing tags
  examples, ngs: added DumpReferenceFASTA.py example
  htsjdk: added code to HTS-JDK  to avoid involving NGS unless we are sure that it is being requested
  ngs, ngs-engine: Added filtering to NGS of secondary alignments that do not have primary alignments
  ngs, test: ngs-python: fixed bug in String processing for Python 3.*
  ngs-engine: ncbi-ngs engine was updated: fixed a bug that made NGS read iterator return 0 reads on WGS accessions.
  ngs: Improved native library load in ngs-java, enhanced its error reporting and added a mode to disable auto-download of native libraries
  ngs: Python code will check for the latest version of the libraries and update if newer ones are available
  ngs: check for the latest version of the libraries and update if newer ones are available
  ngs: simplified ngs-python bindings
