New upstream version 2.9.0

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The NCBI NGS Software Development Kit

Contact: sra-tools@ncbi.nlm.nih.gov

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

# NCBI External Developer Release:

## 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**

If you develop software that relies on `sra-tools`, `ncbi-vdb` or `ngs` in any way, you will likely need to update your code so that it accesses NCBI using HTTPS.

We will be releasing new tools that are HTTPS compatible and `M-15-13` compliant in early September, 2016. Please be certain to update all of your binaries and configuration files.

We have released new tools with version 1.3.0 that are HTTPS compatible and `M-15-13` compliant as of October 7, 2016. Please be certain to [update all of your binaries](https://github.com/ncbi/sra-tools/wiki/Downloads) and configuration files.

# Documentation

ngs-bam: $(LIBDIR) $(OBJDIR) $(LIBDIR)/$(LPFX)ngs-bam.$(SHLX)

ngs-bam-c++: $(LIBDIR) $(OBJDIR) $(LIBDIR)/$(LPFX)ngs-bam-c++.$(LIBX)

ngs-bam-c++:  $(LIBDIR)           $(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX)

$(LIBDIR)/$(LPFX)ngs-bam-c++-static.$(LIBX): $(LIBDIR)/$(LPFX)ngs-bam-c++.$(LIBX)

	rm -f $@

	ln -s $(notdir $^) $@

runtests: ngs-bam ngs-bam-c++

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# NGS-BAM and library version

VERSION = 1.3.0

VERSION = 2.9.0