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rmblast-isb-2.6.0+-changes-vers2.patch
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rmblast-isb-2.6.0+-changes-vers2.patch
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--- tmp/ncbi-blast-2.6.0+-src/c++/src/algo/blast/blastinput/blast_fasta_input.cpp 2016-10-27 12:13:57.000000000 -0700
+++ ncbi-blast-2.6.0+-src/c++/src/algo/blast/blastinput/blast_fasta_input.cpp 2017-02-07 11:56:27.299726089 -0800
@@ -292,6 +292,12 @@ CBlastFastaInputSource::x_InitInputReade
CFastaReader::fAllSeqIds :
(CFastaReader::fNoParseID |
CFastaReader::fDLOptional);
+
+ // Allow CFastaReader fSkipCheck flag to be set based
+ // on new CBlastInputSourceConfig property - GetSkipSeqCheck() -RMH-
+ flags += ( m_Config.GetSkipSeqCheck() ?
+ CFastaReader::fSkipCheck : 0 );
+
flags += (m_ReadProteins
? CFastaReader::fAssumeProt
: CFastaReader::fAssumeNuc);
--- tmp/ncbi-blast-2.6.0+-src/c++/src/algo/blast/blastinput/blast_input.cpp 2016-06-20 08:45:40.000000000 -0700
+++ ncbi-blast-2.6.0+-src/c++/src/algo/blast/blastinput/blast_input.cpp 2017-02-07 11:56:27.300726093 -0800
@@ -53,12 +53,14 @@ CBlastInputSourceConfig::CBlastInputSour
TSeqRange range /* = TSeqRange() */,
bool retrieve_seq_data /* = true */,
int local_id_counter /* = 1 */,
- unsigned int seqlen_thresh2guess /* = numeric_limits<unsigned int>::max()*/ )
+ unsigned int seqlen_thresh2guess /* = numeric_limits<unsigned int>::max()*/,
+ bool skip_seq_check /* = false -RMH- */ )
: m_Strand(strand), m_LowerCaseMask(lowercase),
m_BelieveDeflines(believe_defline), m_Range(range), m_DLConfig(dlconfig),
m_RetrieveSeqData(retrieve_seq_data),
m_LocalIdCounter(local_id_counter),
m_SeqLenThreshold2Guess(seqlen_thresh2guess),
+ m_SkipSeqCheck(skip_seq_check), /* -RMH- */
m_GapsToNs(false)
{
// Set an appropriate default for the strand
--- tmp/ncbi-blast-2.6.0+-src/c++/include/algo/blast/blastinput/blast_input.hpp 2016-06-20 08:45:40.000000000 -0700
+++ ncbi-blast-2.6.0+-src/c++/include/algo/blast/blastinput/blast_input.hpp 2017-02-07 11:56:27.394726411 -0800
@@ -93,6 +93,8 @@ public:
/// type guessing (see @ref kSeqLenThreshold2Guess) [in]
/// @param local_id_counter counter used to create the CSeqidGenerator to
/// create local identifiers for sequences read [in]
+ /// @param skip_seq_check When set this will avoid the sequence
+ /// validation step when using the CFastaReader. -RMH-
CBlastInputSourceConfig(const SDataLoaderConfig& dlconfig,
objects::ENa_strand strand = objects::eNa_strand_other,
bool lowercase = false,
@@ -101,7 +103,8 @@ public:
bool retrieve_seq_data = true,
int local_id_counter = 1,
unsigned int seqlen_thresh2guess =
- numeric_limits<unsigned int>::max());
+ numeric_limits<unsigned int>::max(),
+ bool skip_seq_check = false /* -RMH- */ );
/// Destructor
///
@@ -136,6 +139,18 @@ public:
///
bool GetBelieveDeflines() const { return m_BelieveDeflines; }
+ /// Retrieve status of sequence alphabet validation
+ /// @return boolean to toggle validation of seq data
+ /// -RMH-
+ ///
+ bool GetSkipSeqCheck() const { return m_SkipSeqCheck; }
+
+ /// Turn validation of sequence on/off
+ /// @param skip boolean to toggle validation of sequence
+ /// -RMH-
+ ///
+ void SetSkipSeqCheck(bool skip) { m_SkipSeqCheck = skip; }
+
/// Set range for all sequences
/// @param r range to use [in]
void SetRange(const TSeqRange& r) { m_Range = r; }
@@ -201,6 +216,8 @@ private:
bool m_LowerCaseMask;
/// Whether to parse sequence IDs
bool m_BelieveDeflines;
+ /// Whether to validate sequence data -RMH-
+ bool m_SkipSeqCheck;
/// Sequence range
TSeqRange m_Range;
/// Configuration object for data loaders, used by CBlastInputReader
diff -rupN tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.in ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.in
--- tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.in 1969-12-31 16:00:00.000000000 -0800
+++ ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.in 2017-02-07 11:56:27.408726459 -0800
@@ -0,0 +1,16 @@
+# $Id: Makefile.in 371962 2012-08-14 09:45:56Z coulouri $
+
+# Meta-makefile("APP" project)
+#################################
+
+REQUIRES = objects algo
+
+APP_PROJ = rmblastn
+
+srcdir = @srcdir@
+include @builddir@/Makefile.meta
+
+.PHONY: all $(APP_PROJ)
+
+rmblastn:
+ ${MAKE} ${MFLAGS} -f Makefile.rmblastn_app
diff -rupN tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app
--- tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app 1969-12-31 16:00:00.000000000 -0800
+++ ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app 2017-02-07 11:56:27.426726519 -0800
@@ -0,0 +1,16 @@
+WATCHERS = camacho madden maning
+
+APP = rmblastn
+SRC = rmblastn_app
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+# De-universalize Mac builds to work around a PPC toolchain limitation
+CFLAGS = $(FAST_CFLAGS:ppc=i386)
+CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386)
+LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+CPPFLAGS = $(ORIG_CPPFLAGS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+
+REQUIRES = objects -Cygwin
diff -rupN tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp
--- tmp/ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp 1969-12-31 16:00:00.000000000 -0800
+++ ncbi-blast-2.6.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp 2017-02-07 11:56:27.434726546 -0800
@@ -0,0 +1,183 @@
+/* $Id: rmblastn_app.cpp 371962 2012-08-14 09:45:56Z coulouri $
+ * ===========================================================================
+ *
+ * PUBLIC DOMAIN NOTICE
+ *
+ * ===========================================================================
+ *
+ * Authors: Robert M. Hubley
+ * Christiam Camacho ( original blastn_app.cpp )
+ *
+ */
+
+/** @file rmblastn_app.cpp
+ * RMBLASTN command line application
+ */
+
+#ifndef SKIP_DOXYGEN_PROCESSING
+static char const rcsid[] =
+ "$Id: rmblastn_app.cpp 371962 2012-08-14 09:45:56Z coulouri $";
+#endif /* SKIP_DOXYGEN_PROCESSING */
+
+#include <ncbi_pch.hpp>
+#include <corelib/ncbiapp.hpp>
+#include <algo/blast/api/local_blast.hpp>
+#include <algo/blast/api/remote_blast.hpp>
+#include <algo/blast/blastinput/blast_fasta_input.hpp>
+#include <algo/blast/blastinput/rmblastn_args.hpp>
+#include <algo/blast/api/objmgr_query_data.hpp>
+#include <algo/blast/format/blast_format.hpp>
+#include "../blast/blast_app_util.hpp"
+
+#ifndef SKIP_DOXYGEN_PROCESSING
+USING_NCBI_SCOPE;
+USING_SCOPE(blast);
+USING_SCOPE(objects);
+#endif
+
+class CRMBlastnApp : public CNcbiApplication
+{
+public:
+ /** @inheritDoc */
+ CRMBlastnApp() {
+ CRef<CVersion> version(new CVersion());
+ version->SetVersionInfo(new CBlastVersion());
+ SetFullVersion(version);
+ }
+private:
+ /** @inheritDoc */
+ virtual void Init();
+ /** @inheritDoc */
+ virtual int Run();
+
+ /// This application's command line args
+ CRef<CRMBlastnAppArgs> m_CmdLineArgs;
+};
+
+
+
+void CRMBlastnApp::Init()
+{
+ // formulate command line arguments
+ m_CmdLineArgs.Reset(new CRMBlastnAppArgs());
+
+ // read the command line
+
+ HideStdArgs(fHideLogfile | fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun);
+ SetupArgDescriptions(m_CmdLineArgs->SetCommandLine());
+}
+
+int CRMBlastnApp::Run(void)
+{
+ int status = BLAST_EXIT_SUCCESS;
+
+ try {
+
+ // Allow the fasta reader to complain on invalid sequence input
+ SetDiagPostLevel(eDiag_Warning);
+
+ /*** Get the BLAST options ***/
+ const CArgs& args = GetArgs();
+ CRef<CBlastOptionsHandle> opts_hndl;
+ if(RecoverSearchStrategy(args, m_CmdLineArgs)) {
+ opts_hndl.Reset(&*m_CmdLineArgs->SetOptionsForSavedStrategy(args));
+ }
+ else {
+ opts_hndl.Reset(&*m_CmdLineArgs->SetOptions(args));
+ }
+ const CBlastOptions& opt = opts_hndl->GetOptions();
+
+ /*** Get the query sequence(s) ***/
+ CRef<CQueryOptionsArgs> query_opts =
+ m_CmdLineArgs->GetQueryOptionsArgs();
+ SDataLoaderConfig dlconfig(query_opts->QueryIsProtein());
+ dlconfig.OptimizeForWholeLargeSequenceRetrieval();
+ CBlastInputSourceConfig iconfig(dlconfig, query_opts->GetStrand(),
+ query_opts->UseLowercaseMasks(),
+ query_opts->GetParseDeflines(),
+ query_opts->GetRange());
+ iconfig.SetSkipSeqCheck(true);
+ CBlastFastaInputSource fasta(m_CmdLineArgs->GetInputStream(), iconfig);
+ CBlastInput input(&fasta, m_CmdLineArgs->GetQueryBatchSize());
+
+ /*** Initialize the database/subject ***/
+ CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs());
+ CRef<CLocalDbAdapter> db_adapter;
+ CRef<CScope> scope;
+ InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(),
+ db_adapter, scope);
+ _ASSERT(db_adapter && scope);
+
+ // Initialize the megablast database index now so we can know whether an indexed search will be run.
+ // This is only important for the reference in the report, but would be done anyway.
+ if (opt.GetUseIndex() && !m_CmdLineArgs->ExecuteRemotely()) {
+ CRef<CBlastOptions> my_options(&(opts_hndl->SetOptions()));
+ CSetupFactory::InitializeMegablastDbIndex(my_options);
+ }
+
+ /*** Get the formatting options ***/
+ CRef<CFormattingArgs> fmt_args(m_CmdLineArgs->GetFormattingArgs());
+ CBlastFormat formatter(opt, *db_adapter,
+ fmt_args->GetFormattedOutputChoice(),
+ query_opts->GetParseDeflines(),
+ m_CmdLineArgs->GetOutputStream(),
+ fmt_args->GetNumDescriptions(),
+ fmt_args->GetNumAlignments(),
+ *scope,
+ opt.GetMatrixName(),
+ fmt_args->ShowGis(),
+ fmt_args->DisplayHtmlOutput(),
+ opt.GetQueryGeneticCode(),
+ opt.GetDbGeneticCode(),
+ opt.GetSumStatisticsMode(),
+ m_CmdLineArgs->ExecuteRemotely(),
+ db_adapter->GetFilteringAlgorithm(),
+ fmt_args->GetCustomOutputFormatSpec(),
+ m_CmdLineArgs->GetTask() == "megablast",
+ opt.GetMBIndexLoaded());
+
+
+ formatter.PrintProlog();
+
+ /*** Process the input ***/
+ for (; !input.End(); formatter.ResetScopeHistory()) {
+
+ CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope));
+ CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch));
+
+ SaveSearchStrategy(args, m_CmdLineArgs, queries, opts_hndl);
+
+ CRef<CSearchResultSet> results;
+
+ if (m_CmdLineArgs->ExecuteRemotely()) {
+ CRef<CRemoteBlast> rmt_blast =
+ InitializeRemoteBlast(queries, db_args, opts_hndl,
+ m_CmdLineArgs->ProduceDebugRemoteOutput());
+ results = rmt_blast->GetResultSet();
+ } else {
+ CLocalBlast lcl_blast(queries, opts_hndl, db_adapter);
+ lcl_blast.SetNumberOfThreads(m_CmdLineArgs->GetNumThreads());
+ results = lcl_blast.Run();
+ }
+
+ ITERATE(CSearchResultSet, result, *results) {
+ formatter.PrintOneResultSet(**result, query_batch);
+ }
+ }
+
+ formatter.PrintEpilog(opt);
+
+ if (m_CmdLineArgs->ProduceDebugOutput()) {
+ opts_hndl->GetOptions().DebugDumpText(NcbiCerr, "BLAST options", 1);
+ }
+
+ } CATCH_ALL(status)
+ return status;
+}
+
+#ifndef SKIP_DOXYGEN_PROCESSING
+int main(int argc, const char* argv[] /*, const char* envp[]*/)
+{
+ return CRMBlastnApp().AppMain(argc, argv, 0, eDS_Default, 0);
+}
+#endif /* SKIP_DOXYGEN_PROCESSING */
--- tmp/ncbi-blast-2.6.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp 2016-10-12 07:27:34.000000000 -0700
+++ ncbi-blast-2.6.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp 2017-03-29 11:14:01.852864789 -0700
@@ -1813,6 +1813,9 @@ void CSeqDBImpl::HashToOids(unsigned has
CSeqDBIdSet CSeqDBImpl::GetIdSet()
{
+ // RMH: Added to eliminate race condition for vector garbage collection
+ CFastMutexGuard guard(m_MutexForIdSet);
+
if (m_IdSet.Blank()) {
if (! m_UserGiList.Empty()) {
// Note: this returns a 'blank' IdSet list for positive
--- tmp/ncbi-blast-2.6.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp 2016-02-03 07:19:38.000000000 -0800
+++ ncbi-blast-2.6.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp 2017-03-29 11:12:33.521480161 -0700
@@ -1133,6 +1133,9 @@ public:
private:
CLASS_MARKER_FIELD("IMPL")
+ // RMH
+ CFastMutex m_MutexForIdSet;
+
/// Adjust string length to offset of first embedded NUL byte.
///
/// This is a work-around for bad data in the database; probably