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*~
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.\#*
._*
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
OUTDIR
*.ipch
*.log
/.cproject
/.project
/.pydevproject
.idea/
# mac os x meta-files
.DS_Store
._*
*~
\#*
.\#*
core
*.pyc
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.vscode
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CHANGES deleted 100644 → 0
View file @ 9fc75b68
# ===========================================================================
#
# 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 2.9.0
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
CHANGES.md
View file @ 1e55c85f
# NCBI External Developer Release:
## NGS SDK 2.9.0
## NCBI VDB 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
**February 23, 2018**
**version**: changed version to match that of _ncbi-vdb_
**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
**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
......@@ -13,58 +34,95 @@
**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
## NGS SDK 1.3.0
## 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
**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
**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
**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()
**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-engine**: improved diagnostic messages
**ngs-tools**: Fixed Makefiles to keep supporting "./configure; make" build of sra-search, alongside CMake-based build.
**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 SDK 1.2.5
## NCBI VDB 2.7.0
**July 12, 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
**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
**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()
**ngs**: Fixed a bug in ngs::Alignment::getMateReferenceSpec() affecting pre-March 2015 runs
**ngs**: now supports parallel compilation with "make -j N"
**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
**vfs**: environment variable VDB_PWFILE is no longer used
## NGS SDK 1.2.4
## NCBI VDB 2.6.3
**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.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
**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
LICENSE
View file @ 1e55c85f
......@@ -31,7 +31,18 @@ Please cite the authors in any work or product based on this material.
==============================================================
EXCEPTIONS (in all cases excluding NCBI-written makefiles):
See LICENSE from https://github.com/ncbi/ncbi-vdb
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]
==============================================================
Copyright F.A.Q.
......
Makefile
View file @ 1e55c85f
......@@ -22,42 +22,138 @@
#
# ===========================================================================
# default response to "make"
default: subdirs
# the sub-directories
SUBDIRS = \
ngs-sdk \
ngs-java \
ngs-python \
#-------------------------------------------------------------------------------
# environment
#
TOP ?= $(CURDIR)
include $(TOP)/build/Makefile.shell
SUBDIRS_CLN = \
$(addsuffix _cln,$(SUBDIRS))
SUBDIRS_INST = \
$(addsuffix _inst,$(SUBDIRS))
#-------------------------------------------------------------------------------
# default
#
SUBDIRS = \
libs \
SUBDIRS_TST = \
$(addsuffix _test,$(SUBDIRS))
# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
include $(TOP)/build/Makefile.targets
subdirs: $(SUBDIRS)
default: $(SUBDIRS)
clean: $(SUBDIRS_CLN)
test: $(SUBDIRS)
test: $(SUBDIRS_TST)
$(SUBDIRS) test:
@ $(MAKE) -C $@
install: $(SUBDIRS_INST)
.PHONY: default $(SUBDIRS) test
$(SUBDIRS):
@ $(MAKE) -C $@
#-------------------------------------------------------------------------------
# all
#
$(SUBDIRS_ALL):
#-------------------------------------------------------------------------------
# std
#
$(SUBDIRS_STD):
#-------------------------------------------------------------------------------
# install
#
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
$(SUBDIRS_CLN):
@ $(MAKE) -C $(subst _cln,,$@) clean
#-------------------------------------------------------------------------------
# runtests
#
runtests: runtests_test
runtests_test:
@ $(MAKE) -s -C test runtests
#-------------------------------------------------------------------------------
# slowtests
#
slowtests: slowtests_test
$(SUBDIRS_INST):
@ $(MAKE) -s --no-print-directory -C $(subst _inst,,$@) install
slowtests_test:
@ $(MAKE) -s -C test slowtests
$(SUBDIRS_TST):
@ $(MAKE) -C $(subst _test,,$@) test
#-------------------------------------------------------------------------------
# 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 $@
.PHONY: $(PASSTHRUS) $(RHOSTS) $(REPORTS)
#-------------------------------------------------------------------------------
# configuration help
#
help configure:
@ echo "Before initial build, run 'make OUTDIR=<dir> out' from"
@ echo "the project root to set the output directory of your builds."
@ echo
@ echo "To select a compiler, run 'make <comp>' where"
@ echo "comp = { "$(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
.PHONY: $(SUBDIRS) $(SUBDIRS_CLN) $(SUBDIRS_INST)
.PHONY: help configure
README.md
View file @ 1e55c85f
ngs
===
# The NCBI SRA ( Sequence Read Archive )
# NGS Language Bindings
### Contact:
email: sra-tools@ncbi.nlm.nih.gov
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).
### Change Log
Please check the CHANGES.md file for change history.
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.
## 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.
### 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`.
......@@ -18,8 +21,11 @@ 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 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.
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.
# Documentation
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)
Further documentation is available on the [wiki](https://github.com/ncbi/ngs/wiki).
SRA Toolkit Development Team
build/.gitignore 0 → 100644
View file @ 1e55c85f
.cvsignore
RHOST* ARCH* BUILD* COMP* OUTDIR*
STATIC
ld.linux.exe_cmd.sh
LNKG.*
*.sdf
*.suo
*.user
build/MSVC/2010/bz2.vcxproj 0 → 100644
View file @ 1e55c85f
<?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
build/MSVC/2010/dll-project.props 0 → 100644
View file @ 1e55c85f
<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
build/MSVC/2010/exe-project.props 0 → 100644
View file @ 1e55c85f
<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>
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\ No newline at end of file
build/MSVC/2010/kapp-md.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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</Project>
build/MSVC/2010/kapp.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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</Project>
build/MSVC/2010/ktst-md.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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\ No newline at end of file
build/MSVC/2010/ktst.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<Import Project=".\lib-project.props" />
<Import Project="..\ktst.files" />
</Project>
\ No newline at end of file
build/MSVC/2010/lib-project.props 0 → 100644
View file @ 1e55c85f
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="vdb-common.props" />
<PropertyGroup Label="Configuration">
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\ No newline at end of file
build/MSVC/2010/load.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<Import Project=".\lib-project.props" />
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\ No newline at end of file
build/MSVC/2010/loader.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<Import Project="..\loader.files" />
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\ No newline at end of file
build/MSVC/2010/ncbi-vdb-dll-md.vcxproj 0 → 100644
View file @ 1e55c85f
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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<ItemDefinitionGroup Condition="'$(Configuration)'=='Debug'">
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<Import Project="..\ncbi-vdb-dll.files" />
</Project>
build/MSVC/2010/ncbi-vdb-dll.filters 0 → 100644
View file @ 1e55c85f
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