Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/.gitignore
+++ b/.gitignore
-user.status
-vgcore.*
-/bin64
-/build/COMP.mac
-/build/Makefile.config*
-/build/MSVC/2010/ipch
-/build/MSVC/2010/ncbi-vdb.opensdf
-/centos
-/ilib64
-/lib64
-/mac
-/Makefile.config.mac.arch
-/reconfigure
-/schema
-/test-bin64
-user.status
-/win
-*.opensdf
-*.sdf
-*.suo
 *.log
-/.cproject
-/.project
-/.pydevproject
-
-# mac os x meta-files
-.DS_Store
-._*
-
 *~
 \#*
 .\#*
-core
-*.pyc
-.gdb_history
-.vscode
-.gdb_history
+._*
+
+*.suo
+OUTDIR
+*.ipch
+
+/.cproject
+/.project
+/.pydevproject
+.idea/
--- a/CHANGES
+++ b/CHANGES
+# ===========================================================================
+#
+#                            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.
+#
+#  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
--- a/CHANGES.md
+++ b/CHANGES.md
 # NCBI External Developer Release:

-## NCBI VDB 2.9.1
+
+## 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  
-  **kfg, kns**: Added API to instruct VDB to silently accept any server certificate as valid.  
-  **kfg, vdb-config**: name resolver service now makes use of fcgi  
-  **kfg, vfs**: Fixed a bug that prevented decryption of objects encrypted with non-UTF8 text password keys  
-  **klib**: added check for NULL format argument to string_printf()  
-  **kns**: Randomly select from multiple proxies in configuration  
-  **test**: added Windows test projects for the new schema and the latest vdb  


-## NCBI VDB 2.9.0
+## NGS SDK 2.9.0
 **February 23, 2018**

-  **align**: AlignAccessRefSeqEnumeratorNext no longer filters by the index  
-  **align**: fixed an order-dependent bug affecting cross-table lookups  
-  **build**: Created a script that allows to add a new volume to existing repository  
+  **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  
-  **build**: added "smoke tests"  
-  **build**: recognize version of libhdf5 that does not allow static linking and do not try to use it  
-  **build, doc**: added wiki page: Building-from-source-:--configure-options-explained  
-  **build, ncbi-vdb, sra-tools**: the installation script now saves configuration files if they were modified by the user  
-  **build, vdb-sql**: modified build to avoid vdb-sql in absence of libxml2  
  **kfg**: added searching of configuration files in ../etc/ncbi/ relative to the binaries  
-  **kfg, prefetch**: set limit of Aspera usage to 450m  
-  **kfg, prefetch, remote-fuser, vfs**: Updated resolving of cache location of non-accession objects  
  **kfs**: fix to improve on windows  
  **klib**: Reverted KTimeMakeTime to use UTC  
  **kns**: Accept the same http_proxy specifications as wget  
@@ -34,95 +30,59 @@
  **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**: add ability to make a cache-tee-file without promtion  
  **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  
-  **sra-tools, vdb**: access to vdb/ngs via SQLite  
-  **vdb**: An assert triggered by a rare condition was fixed  
-  **vdb**: new api to estimate pileup-workload based on slice  
-  **vdb**: new function to open HTTP-file with an arbitrary page-size  
-  **vdb**: progressbar can now be created to output on stderr  
  **vfs**: Name resolving service was updated and switched to protocol version 3.0  


-## NCBI VDB 2.8.2
-**March 6, 2017**
-
-  **blast**: Updated blast library to be able to process runs having empty rows  
-  **build**: Added ability to specify ncbi-vdb/configure --with-magic-prefix. Look for libraries in (lib lib64) when running "configure --with-...-prefix"  
-  **build**: configure detects location of ngs libraries  
-  **build**: configure was fixed to skip options unrecognized by gcc 4.4.7  
-  **build**: created sra-toolkit Debian package  
-  **build**: fixed a bug in 'configure' when in could not find source files in repository saved with non-standard name  
-  **build, kfg**: install updates certs.kfg along with other configuration files  
-  **build, ncbi-vdb, sra-tools**: installation will back up old configuration files if they differ from the ones being installed  
-  **kfs, vdb**: Fixes errors occuring when configuration is missing  
-  **klib**: Fixed logging error reported as "log failure: RC(rcText,rcString,rcConverting,rcBuffer,rcInsufficient)"  
-  **kns**: SRA tools respect standard set of environment variables for proxy specification  
-  **kns**: rewrote socket code to use proper local error code switches, especially Windows   
-  **kns**: updated mbedtls library to version 2.4.1  
-  **ncbi-vdb**: configure in detects existence of ngs jar file  
-  **ncbi-vdb, ngs, ngs-tools, sra-tools**: eliminated memcpy from sources due to potential for overlap  
-  **test**: Improved testing framework  
-  **vdb**: increased tenacity in flushing data to disk to accommodate behaviors of file systems such as Lustre.  
-  **vdb-blast**: Implemented vdb-blast API for retrieving reference sequence  
-
-
-## NCBI VDB 2.8.1
-**December 22, 2016**
-
-  **kfg**: added possibility to create an empty KConfig object that does not try to load any file  
-
-
-## NCBI VDB 2.8.0
+## NGS SDK 1.3.0
 **October 7, 2016**

 ### HTTPS-ENABLED RELEASE

-  **kfg, kns**: Use environment variables to determine the proxy for a http protocol  
-  **kfg, vdb-config**: vdb-config-GUI has now option to pick up proxy-setting from environment  
+  **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  
-  **kns**: replaced all direct uses of sleep() within code to enforce standardization upon mS.  
-  **kproc, ncbi-vdb**: Fixed KCondition to generate timeout error on Windows when timeout exhausted  
+  **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  
-  **test**: updated tests to not fail outside of NCBI  
-  **test-sra**: test-sra prints network information  
-  **test-sra**: test-sra prints version of ncbi-vdb or ngs-sdk dynamic library  
-  **vdb**: improved parameter checking on VDatabaseOpenTableRead()  
-  **vdb**: new function: "VDBManagerDeleteCacheOlderThan()"  
-  **vdb**: problem with buffer-overrun when compressing random data fixed  
-  **vdb**: remote/aux nodes have been removed from configuration  
+  **ngs-tools**: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.  


-## NCBI VDB 2.7.0
+## NGS SDK 1.2.5
 **July 12, 2016**

  **blast, kfg, ncbi-vdb, sra-tools, vfs**: restored possibility to disable local caching  
-  **doc, ncbi-vdb**: created a Wiki page illustrating how to use the API to set up logging  
-  **kdb, kfs, kns**: Added blob validation for data being fetched remotely  
+  **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  
-  **kfg**: modified auxiliary remote access configuration to use load-balanced servers  
-  **kns**: Fixed a bug when KHttpRequestPOST generated an incorrect Content-Length after retry  
  **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()  
-  **search**: now supports multi-threaded search  
-  **vdb**: fixed a bug in VCursorFindNextRowIdDirect where it returned a wrong rowId  
-  **vdb**: fixed a bug in the code used to iterate over blobs where rowmap expansion cache would reset iteration to initial row instead of respecting sequence  
+  **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 VDB 2.6.3
+## NGS SDK 1.2.4
 **May 25, 2016**

-  **vdb**: Fixed a bound on memory cache that would never flush under certain access modes  
-
-## NCBI VDB 2.6.2
-**April 20, 2016**
-
-  **kdb**: Fixed VTableDropColumn, so that it can drop static columns  
-  **kfs, kns**: Fixed thread safety issues for both cache and http files  
-  **kproc**: Fixed KQueue to wake waiters when sealed, fixed KSemaphore to wake waiters when canceled  
+  **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.x  
+  **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  
--- a/LICENSE
+++ b/LICENSE
@@ -31,18 +31,7 @@ Please cite the authors in any work or product based on this material.
 ==============================================================
 EXCEPTIONS (in all cases excluding NCBI-written makefiles):

-Location: {libs,interfaces}/ext/bzip2
-Author:   Julian R Seward
-License:  BSDish [libs/ext/bzip2/LICENSE]
-
-Location: {libs,interfaces}/ext/zlib
-Authors:  Jean-loup Gailly and Mark Adler
-License:  BSDish [interfaces/ext/zlib.h]
-
-Location: libs/klib
-Author:   Douglas C. Schmidt
-License:  GNU Lesser General Public [libs/klib/qsort.c]
-
+See LICENSE from https://github.com/ncbi/ncbi-vdb

 ==============================================================
 Copyright F.A.Q.

--- a/Makefile
+++ b/Makefile
@@ -22,138 +22,44 @@
 #
 # ===========================================================================

+# default response to "make"
+default: std

-#-------------------------------------------------------------------------------
-# environment
-#
-TOP ?= $(CURDIR)
-include $(TOP)/build/Makefile.shell
-
+std: subdirs

-#-------------------------------------------------------------------------------
-# default
-#
+# the sub-directories
 SUBDIRS =    \
-	libs \
-
-# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
-include $(TOP)/build/Makefile.targets
+	ngs-sdk \
+	ngs-java \
+	ngs-python \

-default: $(SUBDIRS)
+SUBDIRS_CLN = \
+	$(addsuffix _cln,$(SUBDIRS))

-test: $(SUBDIRS)
+SUBDIRS_INST = \
+	$(addsuffix _inst,$(SUBDIRS))

-$(SUBDIRS) test:
-	@ $(MAKE) -C $@
+SUBDIRS_TST = \
+	$(addsuffix _test,$(SUBDIRS))

-.PHONY: default $(SUBDIRS) test
+subdirs: $(SUBDIRS)

-#-------------------------------------------------------------------------------
-# all
-#
-$(SUBDIRS_ALL):
+clean: $(SUBDIRS_CLN)

-#-------------------------------------------------------------------------------
-# std
-#
-$(SUBDIRS_STD):
+test: $(SUBDIRS_TST)

-#-------------------------------------------------------------------------------
-# install
-#
+install: $(SUBDIRS_INST)

-install: 
-	@ echo "Checking make status of object libraries..."
-	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) $(SUBDIRS)
-	@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install
-
-uninstall:    
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
-
-.PHONY: install uninstall
-
-#-------------------------------------------------------------------------------
-# clean
-#
-clean: clean_test
-
-clean_test:
-	@ $(MAKE) -s -C test clean
-
-#-------------------------------------------------------------------------------
-# runtests
-#
-runtests: runtests_test
-
-runtests_test:
-	@ $(MAKE) -s -C test runtests
-
-#-------------------------------------------------------------------------------
-# slowtests
-#
-slowtests: slowtests_test
-
-slowtests_test:
-	@ $(MAKE) -s -C test slowtests
-
-#-------------------------------------------------------------------------------
-# valgrind
-#
-valgrind: valgrind_test
-
-valgrind_test:
-	@ $(MAKE) -s -C test valgrind
-
-#-------------------------------------------------------------------------------
-# pass-through targets
-#
-COMPILERS = GCC ICC VC++ CLANG
-ARCHITECTURES = i386 x86_64 sparc32 sparc64
-CONFIG = debug profile release
-PUBLISH = scm pubtools
-REPORTS = bindir targdir osdir config compilers architecture architectures
-PASSTHRUS = \
-	out \
-	CC $(COMPILERS) \
-	$(ARCHITECTURES) \
-	$(CONFIG) $(PUBLISH) \
-	purify purecov \
-	local static dynamic
-
-$(RHOSTS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env local
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env require-proxy-exec
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
-
-$(PASSTHRUS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
-
-$(REPORTS):
-	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+$(SUBDIRS):
+	@ $(MAKE) -C $@

-.PHONY: $(PASSTHRUS) $(RHOSTS) $(REPORTS)
+$(SUBDIRS_CLN):
+	@ $(MAKE) -C $(subst _cln,,$@) clean

+$(SUBDIRS_INST):
+	@ $(MAKE) -s --no-print-directory -C $(subst _inst,,$@) install

-#-------------------------------------------------------------------------------
-# configuration help
-#
-help configure:
-	@ echo "Before initial build, run 'make OUTDIR=<dir> out' from"
-	@ echo "the project root to set the output directory of your builds."
-	@ echo
-	@ echo "To select a compiler, run 'make <comp>' where"
-	@ echo "comp = { "$(COMPILERS)" }."
-	@ echo
-	@ echo "For hosts that support cross-compilation ( only Macintosh today ),"
-	@ echo "you can run 'make <arch>' where arch = { "$(ARCHITECTURES)" }."
-	@ echo
-	@ echo "To set a build configuration, run 'make <config>' where"
-	@ echo "config = { "$(CONFIG)" }."
-	@ echo
-	@ echo "To select a remote build configuration, run 'make <rhost>' where"
-	@ echo "rhost = { "$(RHOSTS)" }."
-	@ echo
+$(SUBDIRS_TST):
+	@ $(MAKE) -C $(subst _test,,$@) test

-.PHONY: help configure
+.PHONY: $(SUBDIRS) $(SUBDIRS_CLN) $(SUBDIRS_INST)
--- a/README.md
+++ b/README.md
-# The NCBI SRA ( Sequence Read Archive )
+ngs
+===

-### Contact:
-email: sra-tools@ncbi.nlm.nih.gov
+# NGS Language Bindings

-### Change Log
-Please check the CHANGES.md file for change history.
+NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository [ncbi-vdb](https://github.com/ncbi/ncbi-vdb).

-## NCBI VDB
-The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
-using data in the INSDC Sequence Read Archives.
+The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.

 ### IMPORTANT ANNOUNCEMENT
 As was announced in [OMB memorandum M-15-13](https://www.whitehouse.gov/sites/default/files/omb/memoranda/2015/m-15-13.pdf) on June 8, 2015, NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as `sra-tools`, `ncbi-vdb` or `ngs`.
@@ -21,11 +18,8 @@ If you use software that accesses NCBI SRA data in any way, your software will l
 
 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 have released new tools with version 2.8.0 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.
+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.

-For additional information on using, configuring, and building the toolkit,
-please visit our [wiki](https://github.com/ncbi/sra-tools/wiki)
-or our web site at [NCBI](http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc)
+# Documentation

-
-SRA Toolkit Development Team
+Further documentation is available on the [wiki](https://github.com/ncbi/ngs/wiki).
--- a/build/.gitignore
+++ b/build/.gitignore
-.cvsignore
-RHOST* ARCH* BUILD* COMP* OUTDIR*
-STATIC
-ld.linux.exe_cmd.sh
-LNKG.*
-*.sdf
-*.suo
-*.user
-
-
--- a/build/MSVC/2010/.gitignore
+++ b/build/MSVC/2010/.gitignore
-*.user
-*.suo
-*.sdf
--- a/build/MSVC/2010/bz2.vcxproj
+++ b/build/MSVC/2010/bz2.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-  <Import Project=".\lib-project.props" />  
-  <Import Project="..\bz2.files" />  
-  
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{364EAD74-2052-4D9B-BC8B-43A968A599B0}</ProjectGuid>
-  </PropertyGroup>
-
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/dll-project.props
+++ b/build/MSVC/2010/dll-project.props
-<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">  
-
-  <Import Project="vdb-common.props" />
-  
-  <PropertyGroup Label="Configuration">
-    <ConfigurationType>DynamicLibrary</ConfigurationType>
-    <TargetExt>.dll</TargetExt>
-    <OutDir>$(VDB_TARGET)\bin\</OutDir>
-  </PropertyGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
-  
-  <ItemDefinitionGroup>
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(NGS_ROOT);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName)/win;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      
-      <PreprocessorDefinitions>NO_KRSRC;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <PreprocessorDefinitions>__mod_name__=libs/$(ProjectName);%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <PreprocessorDefinitions>_LIBRARY;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-    <Link>
-      <AdditionalDependencies>Ws2_32.lib;%(AdditionalDependencies)</AdditionalDependencies>
-    </Link>
-  </ItemDefinitionGroup>
-  
-  <ItemDefinitionGroup Condition="'$(Platform)'=='Win32'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/i386;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=32;PKGNAME=win32;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Platform)'=='x64'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/x86_64;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=64;PKGNAME=win64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
-  
-  <ImportGroup Label="ExtensionTargets">
-  </ImportGroup>
-  
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/exe-project.props
+++ b/build/MSVC/2010/exe-project.props
-<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">  
-
-  <Import Project="vdb-common.props" />
-  
-  <PropertyGroup Label="Configuration">
-    <ConfigurationType>Application</ConfigurationType>
-    <TargetExt>.exe</TargetExt>
-    <OutDir>$(VDB_TARGET)\bin\</OutDir>
-  </PropertyGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
-  
-  <ItemDefinitionGroup>
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(NGS_ROOT);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName)/win;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      
-      <PreprocessorDefinitions>WINDOWS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <PreprocessorDefinitions>__mod_name__=test/$(ProjectName);%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      
-      <DisableSpecificWarnings>4290;4251</DisableSpecificWarnings>
-      
-    </ClCompile>
-    <Link>
-      <EntryPointSymbol>wmainCRTStartup</EntryPointSymbol>
-      <AdditionalDependencies>Ws2_32.lib;%(AdditionalDependencies)</AdditionalDependencies>
-    </Link>
-  </ItemDefinitionGroup>
-  
-  <ItemDefinitionGroup Condition="'$(Platform)'=='Win32'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/i386;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=32;PKGNAME=win32;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Platform)'=='x64'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/x86_64;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=64;PKGNAME=win64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  
-  <ItemDefinitionGroup>
-    <Link>
-      <AdditionalDependencies>$(VDB_TARGET)lib\kapp.lib;%(AdditionalDependencies)</AdditionalDependencies>
-    </Link>
-  </ItemDefinitionGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
-  
-  <ImportGroup Label="ExtensionTargets"/>
-
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/kapp-md.vcxproj
+++ b/build/MSVC/2010/kapp-md.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-  <Import Project=".\lib-project.props" />
-  
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Debug'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Release'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  
-  <Import Project="..\kapp.files" />  
-  
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{6964A483-0F5F-459E-AA32-96927BDFB46F}</ProjectGuid>
-  </PropertyGroup>
-</Project>
--- a/build/MSVC/2010/kapp.vcxproj
+++ b/build/MSVC/2010/kapp.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-  <Import Project=".\lib-project.props" />  
-  
-  <Import Project="..\kapp.files" />  
-  
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{FAA69740-AFC2-463C-AAA5-36F768E393C9}</ProjectGuid>
-  </PropertyGroup>
-
-</Project>
--- a/build/MSVC/2010/ktst-md.vcxproj
+++ b/build/MSVC/2010/ktst-md.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{87DB2B3E-916A-478C-AA47-A9907ABBBD54}</ProjectGuid>
-  </PropertyGroup>
-  <Import Project=".\lib-project.props" />
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Debug'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Release'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <Import Project="..\ktst.files" />  
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/ktst.vcxproj
+++ b/build/MSVC/2010/ktst.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{BA319C68-17BF-461E-B018-5736BCDBBE5C}</ProjectGuid>
-  </PropertyGroup>
-  <Import Project=".\lib-project.props" />
-  <Import Project="..\ktst.files" />  
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/lib-project.props
+++ b/build/MSVC/2010/lib-project.props
-<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">  
-
-  <Import Project="vdb-common.props" />
-  
-  <PropertyGroup Label="Configuration">
-    <ConfigurationType>StaticLibrary</ConfigurationType>
-    <TargetExt>.lib</TargetExt>
-    <OutDir>$(VDB_TARGET)\lib\</OutDir>
-  </PropertyGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
-  
-  <ItemDefinitionGroup>
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(NGS_ROOT);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName);%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)libs/$(ProjectName)/win;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      
-      <PreprocessorDefinitions>NO_KRSRC;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <PreprocessorDefinitions>__mod_name__=libs/$(ProjectName);%(PreprocessorDefinitions)</PreprocessorDefinitions>
-      <PreprocessorDefinitions>_LIBRARY;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-    <Link>
-      <EntryPointSymbol>wmainCRTStartup</EntryPointSymbol>
-    </Link>
-  </ItemDefinitionGroup>
-  
-  <ItemDefinitionGroup Condition="'$(Platform)'=='Win32'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/i386;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=32;PKGNAME=win32;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Platform)'=='x64'">
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(VDB_ROOT)interfaces/cc/vc++/x86_64;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <PreprocessorDefinitions>_ARCH_BITS=64;PKGNAME=win64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
-  
-  <ImportGroup Label="ExtensionTargets" />
-  
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/load.vcxproj
+++ b/build/MSVC/2010/load.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-  <Import Project=".\lib-project.props" />  
-  
-  <Import Project="..\load.files" />  
-
-  
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{957B608A-40CB-4A68-98CB-B634F08FA141}</ProjectGuid>
-  </PropertyGroup>
-
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/loader.vcxproj
+++ b/build/MSVC/2010/loader.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-  <Import Project=".\lib-project.props" />  
-  
-  <Import Project="..\loader.files" />  
-
-
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{353472F0-8B23-4DD4-B8FA-F73E0548B5D8}</ProjectGuid>
-  </PropertyGroup>
-
-</Project>
\ No newline at end of file
--- a/build/MSVC/2010/ncbi-vdb-dll-md.vcxproj
+++ b/build/MSVC/2010/ncbi-vdb-dll-md.vcxproj
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Debug|x64">
-      <Configuration>Debug</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|x64">
-      <Configuration>Release</Configuration>
-      <Platform>x64</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  
-    <PropertyGroup Label="Globals">
-        <VDB_TARGET_NAME>ncbi-vdb-md</VDB_TARGET_NAME>
-    </PropertyGroup>
-  <Import Project=".\dll-project.props" />
-  
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Debug'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <ItemDefinitionGroup Condition="'$(Configuration)'=='Release'">
-    <ClCompile>
-      <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
-    </ClCompile>
-  </ItemDefinitionGroup>
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{B74EA4A3-2621-4E61-BCC1-1616FC3F507C}</ProjectGuid>
-  </PropertyGroup>
-  <Import Project="..\ncbi-vdb-dll.files" />  
-</Project>
--- a/build/MSVC/2010/ncbi-vdb-dll.filters
+++ b/build/MSVC/2010/ncbi-vdb-dll.filters