[med-svn] [ncbi-blast+] 02/03: New optionally_keep_sequence patch (#792510).

[Aaron M. Ucko]

This is an automated email from the git hooks/post-receive script.

ucko pushed a commit to branch master
in repository ncbi-blast+.

commit f9e8ec32ff3afb4e215ec46d3c58393329b32c35
Author: Aaron M. Ucko <ucko at debian.org>
Date:   Wed Dec 14 22:44:19 2016 -0500

    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).
---
 debian/changelog                        |  7 ++++++-
 debian/patches/optionally_keep_sequence | 23 +++++++++++++++++++++++
 debian/patches/series                   |  1 +
 3 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index fe9f8da..f22ff11 100644
--- 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 at debian.org>  Wed, 14 Dec 2016 22:37:09 -0500
+ -- Aaron M. Ucko <ucko at 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
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 df091ea..d7a59a6 100644
--- 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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ncbi-blast+.git