New optionally_keep_sequence patch (#792510).

Hang on to sequence data even if -parse_deflines recognized a non-local ID,
on the condition that the environment variable BLAST_ALWAYS_KEEP_SEQUENCE
(or configuration parameter [BLAST] always_keep_sequence) is set to a
"true" value (English-only, case-insensitive true, t, yes, y, or 1).

diff --git a/debian/changelog b/debian/changelog
index fe9f8dac946b0e1ffbaf57e5d518645a8616fb70..f22ff11b7f7f048ea034d839f33caa4d059811c3 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
 ncbi-blast+ (2.5.0-4) UNRELEASED; urgency=medium
 
   * NOT YET RELEASED.
+  * New optionally_keep_sequence patch to hang on to sequence data even if
+    -parse_deflines recognized a non-local ID, on the condition that the
+    environment variable BLAST_ALWAYS_KEEP_SEQUENCE (or configuration
+    parameter [BLAST] always_keep_sequence) is set to a "true" value
+    (English-only, case-insensitive true, t, yes, y, or 1).  (Closes: #792510.)
 
- -- Aaron M. Ucko <ucko@debian.org>  Wed, 14 Dec 2016 22:37:09 -0500
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 14 Dec 2016 22:44:17 -0500
 
 ncbi-blast+ (2.5.0-3) unstable; urgency=medium
 

diff --git a/debian/patches/optionally_keep_sequence b/debian/patches/optionally_keep_sequence
new file mode 100644 (file)
index 0000000..3f01c1e
--- /dev/null
+++ b/debian/patches/optionally_keep_sequence
@@ -0,0 +1,23 @@
+--- a/c++/src/algo/blast/api/search_strategy.cpp
++++ b/c++/src/algo/blast/api/search_strategy.cpp
+@@ -495,6 +495,11 @@ void CExportStrategy::x_Process_Pssm(CRe
+     m_QueueSearchRequest->SetService(new_service);
+ }
+ 
++NCBI_PARAM_DECL(bool, BLAST, always_keep_sequence);
++NCBI_PARAM_DEF_EX(bool, BLAST, always_keep_sequence, false, eParam_Default,
++                  BLAST_ALWAYS_KEEP_SEQUENCE);
++typedef NCBI_PARAM_TYPE(BLAST, always_keep_sequence) TAlwaysKeepSequence;
++
+ void CExportStrategy::x_Process_Query(CRef<IQueryFactory> & query)
+ {
+     if (query.Empty())
+@@ -516,7 +521,7 @@ void CExportStrategy::x_Process_Query(CR
+     // Check if there are any range restrictions applied and if local IDs are
+     // being used to determine how to specify the query sequence(s)
+ 
+-    bool has_local_ids = false;
++    bool has_local_ids = TAlwaysKeepSequence::GetDefault();
+ 
+     if (!seqloc_list.empty())
+     {

diff --git a/debian/patches/series b/debian/patches/series
index df091ea29207e3f39dcd0b5007ebbb6071f7f7de..d7a59a69884d770d7976645326c9cb502a8ea1fe 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -10,3 +10,4 @@ fix_configure
 #support_recent_boost
 support_x32
 suppress_gnutls_version_check
+optionally_keep_sequence