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# ===========================================================================

#

#                            PUBLIC DOMAIN NOTICE

#               National Center for Biotechnology Information

#

#  This software/database is a "United States Government Work" under the

#  terms of the United States Copyright Act.  It was written as part of

#  the author's official duties as a United States Government employee and

#  thus cannot be copyrighted.  This software/database is freely available

#  to the public for use. The National Library of Medicine and the U.S.

#  Government have not placed any restriction on its use or reproduction.

#

#  Although all reasonable efforts have been taken to ensure the accuracy

#  and reliability of the software and data, the NLM and the U.S.

#  Government do not and cannot warrant the performance or results that

#  may be obtained by using this software or data. The NLM and the U.S.

#  Government disclaim all warranties, express or implied, including

#  warranties of performance, merchantability or fitness for any particular

#  purpose.

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#  Please cite the author in any work or product based on this material.

#

# ===========================================================================

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

# NCBI External Developer Release:

## NGS SDK 2.9.4

**January 31, 2019**

  **ngs, ngs-tools**: added an option to skip non-local references  

## 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-BAM and library version

VERSION = 2.9.3

VERSION = 2.9.4

    // TODO: rename to isCircular

    bool getIsCircular() const {

        throw std::runtime_error("not available");

    }

     bool getIsLocal () const {

        throw std::runtime_error("not available");

    }

    uint64_t getLength() const {

        if (state == 2)

        return new ReadCollection::AlignmentSlice(parent, want_primary, want_secondary,

                                                  slice, start, end);

    }

    ngs_adapt::AlignmentItf * getFilteredAlignmentSlice ( int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) const {

        throw std::runtime_error("not available");

    }

    ngs_adapt::PileupItf *getPileups(bool const want_primary, bool const want_secondary) const {

        throw std::runtime_error("not available");

    }