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Author: Aaron M. Ucko <ucko@debian.org>
Date: Wed Dec 14 22:44:19 2016 -0500
Description: 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).
--- a/c++/src/algo/blast/api/search_strategy.cpp
+++ b/c++/src/algo/blast/api/search_strategy.cpp
@@ -560,6 +560,11 @@ 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())
@@ -581,7 +586,7 @@ 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())
{
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