From f9e8ec32ff3afb4e215ec46d3c58393329b32c35 Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Wed, 14 Dec 2016 22:44:19 -0500 Subject: [PATCH] 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(-) create mode 100644 debian/patches/optionally_keep_sequence diff --git a/debian/changelog b/debian/changelog index fe9f8dac..f22ff11b 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 Wed, 14 Dec 2016 22:37:09 -0500 + -- Aaron M. Ucko 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 00000000..3f01c1e5 --- /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 & 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 df091ea2..d7a59a69 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 -- 2.30.2