.gitignore

@@ -12,3 +12,6 @@ OUTDIR
 /.project
 /.pydevproject
 .idea/
+.vscode
+.gdb_history
+core

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

CHANGES.md

 # 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_
 
 

debian/changelog

+ngs-sdk (2.9.4-1) UNRELEASED; urgency=medium
+
+  * New upstream version 2.9.4
+
+ -- Andrius Merkys <andrius.merkys@gmail.com>  Sun, 10 Mar 2019 04:15:10 -0400
+
 ngs-sdk (2.9.3-1) unstable; urgency=medium
 
   * New upstream version

ngs-bam/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-BAM and library version
-VERSION = 2.9.3
+VERSION = 2.9.4

ngs-bam/ngs-bam.cpp

@@ -327,6 +327,9 @@ public:
     // 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)
@@ -371,6 +374,9 @@ public:
         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");
     }

ngs-java/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-JAVA and library version
-VERSION = 2.9.3
+VERSION = 2.9.4

ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java

@@ -29,6 +29,6 @@ package gov.nih.nlm.ncbi.ngs;
 class LibDependencies {
     final static String NGS_SDK  = "ngs-sdk";
     final static String NCBI_VDB = "ncbi-vdb";
-    final static String NGS_SDK_VERSION = "2.9.2";
-    final static String NCBI_VDB_VERSION = "2.9.1";
+    final static String NGS_SDK_VERSION = "2.9.4";
+    final static String NCBI_VDB_VERSION = "2.9.4";
 }

ngs-java/ngs/Reference.java

@@ -59,6 +59,17 @@ public interface Reference
         throws ErrorMsg;
 
 
+    /**
+     * getIsLocal
+     * @return true if Reference is stored locally within the ReadCollection.
+     *          Unique Reference sequences are stored locally, while  Publicly available Reference sequences are stored externally.
+     *          An exception to this rule is when a public Reference is small,  in which case the sequence will be available both locally and externally
+	 * @throws ErrorMsg if cannot detect if reference is local
+     */
+    boolean getIsLocal ()
+        throws ErrorMsg;
+
+
     /**
      * getLength
      * @return the length of the reference sequence
@@ -116,7 +127,6 @@ public interface Reference
     String getReferenceChunk ( long offset, long length )
         throws ErrorMsg;
 
-
     /*----------------------------------------------------------------------
      * ALIGNMENTS
      */

ngs-java/ngs/itf/ReferenceItf.java

@@ -75,6 +75,16 @@ class ReferenceItf
     }
 
 
+    /* getIsLocal
+     *  returns true if reference is local
+     */
+    public boolean getIsLocal ()
+        throws ErrorMsg
+    {
+        return this . GetIsLocal ( self );
+    }
+
+
     /* getLength
      *  returns the length of the reference sequence
      */
@@ -344,6 +354,8 @@ class ReferenceItf
         throws ErrorMsg;
         private native boolean GetIsCircular ( long self )
         throws ErrorMsg;
+    private native boolean GetIsLocal ( long self )
+        throws ErrorMsg;
     private native long GetLength ( long self )
         throws ErrorMsg;
     private native String GetReferenceBases ( long self, long offset, long length )

ngs-python/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-PYTHON and library version
-VERSION = 2.9.3
+VERSION = 2.9.4

ngs-python/ngs/LibManager.py

@@ -371,6 +371,7 @@ class LibManager:
         self.bind_sdk("PY_NGS_ReferenceGetCommonName",             [c_void_p, POINTER(c_void_p), POINTER(c_void_p)])
         self.bind_sdk("PY_NGS_ReferenceGetCanonicalName",          [c_void_p, POINTER(c_void_p), POINTER(c_void_p)])
         self.bind_sdk("PY_NGS_ReferenceGetIsCircular",             [c_void_p, POINTER(c_int), POINTER(c_void_p)])
+        self.bind_sdk("PY_NGS_ReferenceGetIsLocal",                [c_void_p, POINTER(c_int), POINTER(c_void_p)])
         self.bind_sdk("PY_NGS_ReferenceGetLength",                 [c_void_p, POINTER(c_uint64), POINTER(c_void_p)])
         self.bind_sdk("PY_NGS_ReferenceGetReferenceBases",         [c_void_p, c_uint64, c_uint64, POINTER(c_void_p), POINTER(c_void_p)])
         self.bind_sdk("PY_NGS_ReferenceGetReferenceChunk",         [c_void_p, c_uint64, c_uint64, POINTER(c_void_p), POINTER(c_void_p)])

ngs-python/ngs/Reference.py

@@ -52,6 +52,9 @@ class Reference(Refcount):
     def getIsCircular(self):
         return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsCircular, c_int))
 
+    def getIsLocal(self):
+        return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsLocal, c_int))
+
     def getLength(self):
         return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetLength, c_uint64)
 

ngs-sdk/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-SDK and library version
-VERSION = 2.9.3
+VERSION = 2.9.4

ngs-sdk/adapter/ErrorMsg.cpp

@@ -38,7 +38,7 @@ namespace ngs_adapt
      *  what went wrong
      */
     const char * ErrorMsg :: what () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg . c_str ();
     }
@@ -47,7 +47,7 @@ namespace ngs_adapt
      *  returns the detailed message
      */
     const :: std :: string & ErrorMsg :: toMessage () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg;
     }
@@ -56,7 +56,7 @@ namespace ngs_adapt
      *  returns a short description
      */
     const :: std :: string & ErrorMsg :: toString () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg;
     }
@@ -65,24 +65,24 @@ namespace ngs_adapt
      *  various means of constructing
      */
     ErrorMsg :: ErrorMsg ()
-        throw ()
+        NGS_NOTHROW ()
     {
     }
 
     ErrorMsg :: ErrorMsg ( const :: std :: string & message )
-            throw ()
+            NGS_NOTHROW ()
         : msg ( message )
     {
     }
 
     ErrorMsg :: ErrorMsg ( const ErrorMsg & obj )
-            throw ()
+            NGS_NOTHROW ()
         : msg ( obj . msg )
     {
     }
 
     ErrorMsg & ErrorMsg :: operator = ( const ErrorMsg & obj )
-        throw ()
+        NGS_NOTHROW ()
     {
         this -> msg = obj . msg;
         return * this;
@@ -90,7 +90,7 @@ namespace ngs_adapt
 
 
     ErrorMsg :: ~ ErrorMsg ()
-        throw ()
+        NGS_NOTHROW ()
     {
     }
 

ngs-sdk/adapter/ReferenceItf.cpp

@@ -92,6 +92,21 @@ namespace ngs_adapt
         return 0;
     }
 
+    bool CC ReferenceItf :: is_local ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err )
+    {
+        const ReferenceItf * self = Self ( iself );
+        try
+        {
+            return self -> getIsLocal ();
+        }
+        catch ( ... )
+        {
+            ErrBlockHandleException ( err );
+        }
+
+        return 0;
+    }
+
     uint64_t CC ReferenceItf :: get_length ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err )
     {
         const ReferenceItf * self = Self ( iself );
@@ -141,6 +156,22 @@ namespace ngs_adapt
         return 0;
     }
 
+    uint64_t CC ReferenceItf :: get_alignment_count ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err,
+            bool wants_primary, bool wants_secondary )
+    {
+        const ReferenceItf * self = Self ( iself );
+        try
+        {
+            return self -> getAlignmentCount ( wants_primary, wants_secondary );
+        }
+        catch ( ... )
+        {
+            ErrBlockHandleException ( err );
+        }
+
+        return 0;
+    }
+
     NGS_Alignment_v1 * CC ReferenceItf :: get_alignment ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err,
             const char * alignmentId )
     {
@@ -192,6 +223,23 @@ namespace ngs_adapt
         return 0;
     }
 
+    NGS_Alignment_v1 * CC ReferenceItf :: get_filtered_align_slice ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err,
+                                            int64_t start, uint64_t length, uint32_t flags, int32_t map_qual )
+    {
+        const ReferenceItf * self = Self ( iself );
+        try
+        {
+            AlignmentItf * val = self -> getFilteredAlignmentSlice ( start, length, flags, map_qual );
+            return val -> Cast ();
+        }
+        catch ( ... )
+        {
+            ErrBlockHandleException ( err );
+        }
+
+        return 0;
+    }
+
     NGS_Pileup_v1 * CC ReferenceItf :: get_pileups ( const NGS_Reference_v1 * iself, NGS_ErrBlock_v1 * err,
                                      bool wants_primary, bool wants_secondary )
     {
@@ -280,7 +328,7 @@ namespace ngs_adapt
         {
             "ngs_adapt::ReferenceItf",
             "NGS_Reference_v1",
-            1,
+            4,
             & OpaqueRefcount :: ivt . dad
         },
 
@@ -300,7 +348,17 @@ namespace ngs_adapt
 
         // 1.1
         get_filtered_pileups,
-        get_filtered_pileup_slice
+        get_filtered_pileup_slice,
+
+        // 1.2
+        get_alignment_count,
+
+        // 1.3 interface
+        NULL,// get_filtered_alignments (not exposed via ngs::Reference)
+        get_filtered_align_slice,
+
+        // 1.4
+        is_local
     };
 
 } // namespace ngs_adapt

ngs-sdk/dispatch/AlignmentItf.cpp

@@ -61,7 +61,7 @@ namespace ngs
      */
 
     StringItf * AlignmentItf :: getAlignmentId () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -81,7 +81,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getReferenceSpec () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -101,7 +101,7 @@ namespace ngs
     }
 
     int32_t AlignmentItf :: getMappingQuality () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -121,7 +121,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getReferenceBases () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -141,7 +141,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getReadGroup () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -161,7 +161,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getReadId () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -181,7 +181,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getClippedFragmentBases () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -201,7 +201,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getClippedFragmentQualities () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -221,7 +221,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getAlignedFragmentBases () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -241,7 +241,7 @@ namespace ngs
     }
 
     uint32_t AlignmentItf :: getAlignmentCategory () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -261,7 +261,7 @@ namespace ngs
     }
 
     int64_t AlignmentItf :: getAlignmentPosition () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -281,7 +281,7 @@ namespace ngs
     }
 
     uint64_t AlignmentItf :: getReferencePositionProjectionRange (int64_t ref_pos) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -305,7 +305,7 @@ namespace ngs
     }
 
     uint64_t AlignmentItf :: getAlignmentLength () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -325,7 +325,7 @@ namespace ngs
     }
 
     bool AlignmentItf :: getIsReversedOrientation () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -345,7 +345,7 @@ namespace ngs
     }
 
     int32_t AlignmentItf :: getSoftClip ( uint32_t edge ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -365,7 +365,7 @@ namespace ngs
     }
 
     uint64_t AlignmentItf :: getTemplateLength () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -385,7 +385,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getShortCigar ( bool clipped ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -405,7 +405,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getLongCigar ( bool clipped ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -425,7 +425,7 @@ namespace ngs
     }
 
     char AlignmentItf :: getRNAOrientation () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -449,7 +449,7 @@ namespace ngs
     }
 
     bool AlignmentItf :: hasMate () const
-        throw ()
+        NGS_NOTHROW ()
     {
         try
         {
@@ -482,7 +482,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getMateAlignmentId () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -502,7 +502,7 @@ namespace ngs
     }
 
     AlignmentItf * AlignmentItf :: getMateAlignment () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -522,7 +522,7 @@ namespace ngs
     }
 
     StringItf * AlignmentItf :: getMateReferenceSpec () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -542,7 +542,7 @@ namespace ngs
     }
 
     bool AlignmentItf :: getMateIsReversedOrientation () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Alignment_v1 * self = Test ();
@@ -562,7 +562,7 @@ namespace ngs
     }
 
     bool AlignmentItf :: nextAlignment ()
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         NGS_Alignment_v1 * self = Test ();

ngs-sdk/dispatch/ErrBlock.cpp

@@ -34,7 +34,7 @@ namespace ngs
      */
 
     void ErrBlock :: Throw () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         if ( xtype != xt_okay )
             throw ErrorMsg ( msg );

ngs-sdk/dispatch/ErrorMsg.cpp

@@ -38,7 +38,7 @@ namespace ngs
      *  what went wrong
      */
     const char * ErrorMsg :: what () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg . c_str ();
     }
@@ -47,7 +47,7 @@ namespace ngs
      *  returns the detailed message
      */
     const :: std :: string & ErrorMsg :: toMessage () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg;
     }
@@ -56,7 +56,7 @@ namespace ngs
      *  returns a short description
      */
     const :: std :: string & ErrorMsg :: toString () const
-        throw ()
+        NGS_NOTHROW ()
     {
         return msg;
     }
@@ -65,31 +65,31 @@ namespace ngs
      *  various means of constructing
      */
     ErrorMsg :: ErrorMsg ()
-        throw ()
+        NGS_NOTHROW ()
     {
     }
 
     ErrorMsg :: ErrorMsg ( const :: std :: string & message )
-            throw ()
+            NGS_NOTHROW ()
         : msg ( message )
     {
     }
 
     ErrorMsg :: ErrorMsg ( const ErrorMsg & obj )
-            throw ()
+            NGS_NOTHROW ()
         : msg ( obj . msg )
     {
     }
 
     ErrorMsg & ErrorMsg :: operator = ( const ErrorMsg & obj )
-        throw ()
+        NGS_NOTHROW ()
     {
         this -> msg = obj . msg;
         return * this;
     }
 
     ErrorMsg :: ~ ErrorMsg ()
-        throw ()
+        NGS_NOTHROW ()
     {
     }
 

ngs-sdk/dispatch/FragmentItf.cpp

@@ -58,7 +58,7 @@ namespace ngs
      */
 
     StringItf * FragmentItf :: getFragmentId () const
-            throw ( ErrorMsg )
+            NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Fragment_v1 * self = Test ();
@@ -78,19 +78,19 @@ namespace ngs
     }
 
     StringItf * FragmentItf :: getFragmentBases () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         return this -> getFragmentBases ( 0, -1 );
     }
 
     StringItf * FragmentItf :: getFragmentBases ( uint64_t offset ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         return this -> getFragmentBases ( offset, -1 );
     }
 
     StringItf * FragmentItf :: getFragmentBases ( uint64_t offset, uint64_t length ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Fragment_v1 * self = Test ();
@@ -110,19 +110,19 @@ namespace ngs
     }
 
     StringItf * FragmentItf :: getFragmentQualities () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         return this -> getFragmentQualities ( 0, -1 );
     }
 
     StringItf * FragmentItf :: getFragmentQualities ( uint64_t offset ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         return this -> getFragmentQualities ( offset, -1 );
     }
 
     StringItf * FragmentItf :: getFragmentQualities ( uint64_t offset, uint64_t length ) const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Fragment_v1 * self = Test ();
@@ -142,7 +142,7 @@ namespace ngs
     }
 
     bool FragmentItf :: nextFragment ()
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         NGS_Fragment_v1 * self = Test ();
@@ -162,7 +162,7 @@ namespace ngs
     }
 
     bool FragmentItf :: isPaired () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Fragment_v1 * self = Test ();
@@ -186,7 +186,7 @@ namespace ngs
     }
 
     bool FragmentItf :: isAligned () const
-        throw ( ErrorMsg )
+        NGS_THROWS ( ErrorMsg )
     {
         // the object is really from C
         const NGS_Fragment_v1 * self = Test ();