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


NGS SDK 2.9.3
October 17, 2018

  ngs: changed version to match that of ncbi-vdb


NGS SDK 2.9.2
July 23, 2018

  ngs: changed version to match that of ncbi-vdb


NGS SDK 2.9.1
June 15, 2018

  build: 'make install' ignore ROOT environment variable


NGS SDK 2.9.0
February 23, 2018

  version: changed version to match that of ncbi-vdb
  build: Fixed configure allowing to run it on Perl with version >= v5.26 that has "." removed from @INC  
  kfg: added searching of configuration files in ../etc/ncbi/ relative to the binaries  
  kfs: fix to improve on windows  
  klib: Reverted KTimeMakeTime to use UTC  
  kns: Accept the same http_proxy specifications as wget  
  kns: Added possibility to report server's IP address after network error  
  kns: Ignore HTTP headers sent multiple times  
  kns: Improved reporting of network errors  
  kns: fixed generation of invalid error code in response to dropped connection  
  ncbi-vdb: fixed bug of directory not found on mac  
  ncbi-vdb, ngs-engine: improved handling of blobs inside the NGS engine   
  ngs: Examples for python 2.6 were removed  
  ngs: Python examples work with Python 2.6.6  
  ngs-engine: improved performance when iterating through partially aligned and unaligned reads  
  ngs-engine: optimized filtered access to unaligned runs  
  vfs: Name resolving service was updated and switched to protocol version 3.0  

NGS SDK 1.3.0
October 7, 2016

HTTPS-ENABLED RELEASE

  build, ngs-tools: Now ngs-tools look for its dependencies using their normal build paths and does not reconfigure them  
  build, ngs-tools: Now ngs-tools use CMAKE_INSTALL_PREFIX for installation path  
  kns: All tools and libraries now support https  
  ngs: Fixed all crashes when using null as string in ngs-java APIs  
  ngs: NGS_ReferenceGetChunk() will now return chunks potentially exceeding 5000 bases  
  ngs: fixed potential concurrency issues at exit, when called from Java  
  ngs: ngs-java and ngs-python auto-download (of native libraries) now works through HTTPS  
  ngs: read fragments of length 0 are now ignored  
  ngs, ngs-tools, ref-variation: added class ngs-vdb::VdbAlignment, featuring method IsFirst()  
  ngs-engine: improved diagnostic messages  
  ngs-tools: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.  


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


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
