VDB-4434: 2.11.0 RELEASE: Merge branch '2.11.0rc'

ZLJLZX · Mar 15, 2021 · e2117ad · e2117ad
2 parents 10f288b + 40d8df5
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,6 +1,30 @@
 # NCBI External Developer Release:
 
 
+## SRA Toolkit 2.11.0
+**March 15, 2021**
+
+  **fasterq-dump**: does not exit with 0 any more if the given path is not found  
+  **fasterq-dump**: does not exit with 0 if accession is not found  
+  **fasterq-dump**: does not fail when requested to dump a run file with non-standard name  
+  **fasterq-dump**: available on windows  
+  **kfg, prefetch, vfs**: resolve WGS reference sequences into "Accession Directory"  
+  **kfg, sra-tools, vfs**: dropped support of protected repositories  
+  **kns, sra-tools**: fixed formatting of HTTP requests for proxy  
+  **ncbi-vdb, ngs, ngs-tools, sra-tools, vdb**: added support for 64-bit ARM (AArch64, Apple Silicon)  
+  **prefetch, vfs**: fixed download of protected non-run files  
+  **prefetch, vfs**: fixed segfault during download of JWT cart  
+  **prefetch, vfs**: respect requested version when downloading WGS files  
+  **sra-pileup**: now silent if requested slice has no alignments or reference-name does not exist  
+  **sratools**: added description and documentation of the sratools driver tool to GitHub wiki  
+  **sra-tools**: created a script to fix names of downloaded sra files  
+  **sra-tools**: created a script to move downloaded sra run files into proper directories  
+  **sratools**: disable-multithreading option removed from help text for tools that do not support it  
+  **sratools**: does not access remote repository when it is disabled  
+  **sra-tools, vfs**: recognize sra file names with version  
+  **vdb-dump**: exits with no-zero value if asked for non existing column  
+
+
 ## SRA Toolkit 2.10.9
 **December 16, 2020**
 

diff --git a/README.md b/README.md
@@ -16,6 +16,28 @@ using data in the INSDC Sequence Read Archives.
 ### ANNOUNCEMENT:
 NIH has released a request for information (RFI) to solicit community feedback on new proposed Sequence Read Archive (SRA) data formats. Learn more and share your thoughts at https://go.usa.gov/xvhdr. The response deadline is July 17th, 2020. We’d encourage you all to share with your colleagues and networks, and respond if you are an SRA submitter or data user.
 
+SRA Toolkit 2.11.0 March 15, 2021
+
+  **fasterq-dump**: does not exit with 0 any more if the given path is not found  
+  **fasterq-dump**: does not exit with 0 if accession is not found  
+  **fasterq-dump**: does not fail when requested to dump a run file with non-standard name  
+  **fasterq-dump**: available on windows  
+  **kfg, prefetch, vfs**: resolve WGS reference sequences into "Accession Directory"  
+  **kfg, sra-tools, vfs**: dropped support of protected repositories  
+  **kns, sra-tools**: fixed formatting of HTTP requests for proxy  
+  **ncbi-vdb, ngs, ngs-tools, sra-tools, vdb**: added support for 64-bit ARM (AArch64, Apple Silicon)  
+  **prefetch, vfs**: fixed download of protected non-run files  
+  **prefetch, vfs**: fixed segfault during download of JWT cart  
+  **prefetch, vfs**: respect requested version when downloading WGS files  
+  **sra-pileup**: now silent if requested slice has no alignments or reference-name does not exist  
+  **sratools**: added description and documentation of the sratools driver tool to GitHub wiki  
+  **sra-tools**: created a script to fix names of downloaded sra files  
+  **sra-tools**: created a script to move downloaded sra run files into proper directories  
+  **sratools**: disable-multithreading option removed from help text for tools that do not support it  
+  **sratools**: does not access remote repository when it is disabled  
+  **sra-tools, vfs**: recognize sra file names with version  
+  **vdb-dump**: exits with no-zero value if asked for non existing column  
+
 SRA Toolkit 2.10.8
 
 kproc, fasterq-dump: fixed problem with seg-faults caused by too small stack used by threads

diff --git a/build/MSVC/2010/fasterq-dump.vcxproj b/build/MSVC/2010/fasterq-dump.vcxproj
@@ -0,0 +1,35 @@
+<?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=".\exe-project.props" />
+
+  <ItemDefinitionGroup>
+    <Link>
+      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
+    </Link>
+  </ItemDefinitionGroup>
+  <Import Project="..\fasterq-dump.files" />
+
+  <PropertyGroup Label="Globals">
+    <ProjectGuid>{2182DDEE-BE67-48FB-89BA-9EF23717C128}</ProjectGuid>
+  </PropertyGroup>
+
+</Project>
diff --git a/build/MSVC/2013/fasterq-dump.vcxproj b/build/MSVC/2013/fasterq-dump.vcxproj
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project=".\exe-project.props" />
+
+  <ItemDefinitionGroup>
+    <Link>
+      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
+    </Link>
+  </ItemDefinitionGroup>
+  <Import Project="..\fasterq-dump.files" />
+
+  <PropertyGroup Label="Globals">
+    <ProjectGuid>{2182DDEE-BE67-48FB-89BA-9EF23717C128}</ProjectGuid>
+  </PropertyGroup>
+
+</Project>
diff --git a/build/MSVC/2017/driver-tool.vcxproj b/build/MSVC/2017/driver-tool.vcxproj
@@ -1,39 +1,41 @@
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <PropertyGroup Label="Configuration">
-    <TargetName>sratools</TargetName>
-  </PropertyGroup>
-  <Import Project=".\exe-project.props" />
-  <ItemDefinitionGroup>
-    <ClCompile>
-      <AdditionalIncludeDirectories>$(ProjectDir)../../../tools/driver-tool/inc/;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
-      <AdditionalOptions>/Zc:__cplusplus %(AdditionalOptions)</AdditionalOptions>
-    </ClCompile>
-    <Link>
-      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
-    </Link>
-    <PostBuildEvent>
-      <Command>
-            del $(TargetDir)$(TargetName).lib
-            del $(TargetDir)$(TargetName).exp
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)fastq-dump$(TargetExt)
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)fastq-dump.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)sam-dump$(TargetExt)
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)sam-dump.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)sra-pileup$(TargetExt)
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)sra-pileup.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)vdb-dump$(TargetExt)
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)vdb-dump.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)prefetch$(TargetExt)
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)prefetch.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)srapath.pdb
-            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)srapath$(TargetExt)
-        </Command>
-    </PostBuildEvent>
-  </ItemDefinitionGroup>
-  <Import Project="..\driver-tool.files" />
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{C2C78E19-90A8-4CC5-8A15-DFC7447E3576}</ProjectGuid>
-    <WindowsTargetPlatformVersion>10.0.17763.0</WindowsTargetPlatformVersion>
-  </PropertyGroup>
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <PropertyGroup Label="Configuration">
+    <TargetName>sratools</TargetName>
+  </PropertyGroup>
+  <Import Project=".\exe-project.props" />
+  <ItemDefinitionGroup>
+    <ClCompile>
+      <AdditionalIncludeDirectories>$(ProjectDir)../../../tools/driver-tool/inc/;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+      <AdditionalOptions>/Zc:__cplusplus %(AdditionalOptions)</AdditionalOptions>
+    </ClCompile>
+    <Link>
+      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
+    </Link>
+    <PostBuildEvent>
+      <Command>
+            del $(TargetDir)$(TargetName).lib
+            del $(TargetDir)$(TargetName).exp
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)fastq-dump$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)fastq-dump.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)sam-dump$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)sam-dump.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)sra-pileup$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)sra-pileup.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)vdb-dump$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)vdb-dump.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)prefetch$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)prefetch.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)srapath$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)srapath.pdb
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName)$(TargetExt)  $(TargetDir)fasterq-dump$(TargetExt)
+            echo f | xcopy /F /Y $(TargetDir)$(TargetName).pdb          $(TargetDir)fasterq-dump.pdb
+        </Command>
+    </PostBuildEvent>
+  </ItemDefinitionGroup>
+  <Import Project="..\driver-tool.files" />
+  <PropertyGroup Label="Globals">
+    <ProjectGuid>{C2C78E19-90A8-4CC5-8A15-DFC7447E3576}</ProjectGuid>
+    <WindowsTargetPlatformVersion>10.0.17763.0</WindowsTargetPlatformVersion>
+  </PropertyGroup>
 </Project>
diff --git a/build/MSVC/2017/fasterq-dump.vcxproj b/build/MSVC/2017/fasterq-dump.vcxproj
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+    <PropertyGroup Label="Configuration">
+        <TargetName>fasterq-dump-orig</TargetName>
+    </PropertyGroup>
+  <Import Project=".\exe-project.props" />
+  <ItemDefinitionGroup>
+    <Link>
+      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
+    </Link>
+  </ItemDefinitionGroup>
+  <Import Project="..\fasterq-dump.files" />
+  <PropertyGroup Label="Globals">
+    <ProjectGuid>{97827B04-8AB2-498B-8971-F73D6CF8B2EC}</ProjectGuid>
+  </PropertyGroup>
+</Project>
diff --git a/build/MSVC/2017/fastq-dump-ngs.vcxproj b/build/MSVC/2017/fastq-dump-ngs.vcxproj
@@ -4,7 +4,7 @@
   <ItemDefinitionGroup>
     <Link>
       <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-vdb.lib;%(AdditionalDependencies)</AdditionalDependencies>
-      <AdditionalDependencies>$(VDB_TARGET)lib\ngs-c++.lib;%(AdditionalDependencies)</AdditionalDependencies>
+      <AdditionalDependencies>$(VDB_TARGET)lib\ncbi-ngs.lib;%(AdditionalDependencies)</AdditionalDependencies>
       <AdditionalDependencies>$(NGS_TARGET)lib\libngs-bind-c++.lib;%(AdditionalDependencies)</AdditionalDependencies>
       <AdditionalDependencies>$(NGS_TARGET)lib\libngs-disp.lib;%(AdditionalDependencies)</AdditionalDependencies>
     </Link>