Remove duplicate alphabets and replace seqan2::String

.gitmodules

@@ -11,9 +11,6 @@
 [submodule "lib/raptor_data_simulation"]
 	path = lib/raptor_data_simulation
 	url = git@github.com:eaasna/raptor_data_simulation.git
-[submodule "lib/stellar3"]
-	path = lib/stellar3
-	url = git@github.com:seqan/stellar3.git
 [submodule "lib/seqan"]
 	path = lib/seqan
 	url = git@github.com:seqan/seqan.git

CMakeLists.txt

@@ -19,6 +19,12 @@ set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set (CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 
+# For debugging only
+#set (CMAKE_CXX_FLAGS "-ftemplate-backtrace-limit=0")
+#set (CMAKE_CXX_FLAGS "-fsanitize=address -g -O0")
+set (CMAKE_CXX_FLAGS "-g -O0 -Wno-unused-parameter -Wno-unused-value -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unused-local-typedefs")
+
+
 # Messages
 string (ASCII 27 Esc)
 set (FontBold "${Esc}[1m")

include/dream_stellar/LICENSE.md

@@ -0,0 +1,22 @@
+// ==========================================================================
+//                    STELLAR - SwifT Exact LocaL AligneR
+//                   http://www.seqan.de/projects/stellar/
+// ==========================================================================
+// Copyright (C) 2010-2012 by Birte Kehr
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 3 of the License, or (at your options) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ==========================================================================
+// Author: Birte Kehr <birte.kehr@fu-berlin.de>
+// ==========================================================================

include/dream_stellar/diagnostics/print.hpp

@@ -0,0 +1,60 @@
+#pragma once
+
+#include <dream_stellar/stellar_types.hpp>
+#include <dream_stellar/stellar_output.hpp>
+
+namespace dream_stellar
+{
+
+///////////////////////////////////////////////////////////////////////////////
+// Calculates parameters from parameters in options object and writes them to outStr
+// Sets options.qGram if not set by user input
+template <typename TStream>
+void _writeCalculatedParams(StellarOptions & options, TStream & outStr);
+
+///////////////////////////////////////////////////////////////////////////////
+// Writes user specified parameters from options object to outStr
+template <typename TStream>
+void _writeSpecifiedParams(StellarOptions const & options, TStream & outStr);
+
+///////////////////////////////////////////////////////////////////////////////
+// Writes file name from options object to outStr
+template <typename TStream>
+void _writeFileNames(StellarOptions const & options, TStream & outStr);
+
+///////////////////////////////////////////////////////////////////////////////
+// Calculates parameters from parameters in options object and from sequences and writes them to outStr
+template <typename sequence_t, typename TStream>
+void _writeMoreCalculatedParams(StellarOptions const & options,
+                                uint64_t const & refLen,
+                                std::vector<sequence_t> const & queries,
+                                TStream & outStr);
+
+void _writeOutputStatistics(StellarOutputStatistics const & statistics, bool const verbose, bool const writeDisabledQueriesFile);
+
+template <typename TStream>
+void _printStellarKernelStatistics(StellarComputeStatistics const & statistics, TStream & outStr);
+
+template <typename TStream>
+void _printDatabaseIdAndStellarKernelStatistics(
+    bool const verbose,
+    bool const databaseStrand,
+    CharString const & databaseID,
+    StellarComputeStatistics const & statistics,
+    TStream & outStr);
+
+template <typename TStream>
+void _printStellarStatistics(
+    bool const verbose,
+    bool const databaseStrand,
+    StringSet<CharString> const & databaseIDs,
+    StellarComputeStatisticsCollection const & computeStatistics,
+    TStream & outStr);
+
+template <typename TStream>
+void _writeOutputStatistics(StellarOutputStatistics const & statistics,
+                            bool const verbose,
+                            bool const writeDisabledQueriesFile,
+                            TStream & outStr);
+
+} // namespace dream_stellar

include/dream_stellar/diagnostics/print.tpp

@@ -0,0 +1,182 @@
+#pragma once
+
+#include <dream_stellar/diagnostics/print.hpp>
+
+namespace dream_stellar
+{
+
+using namespace seqan2;
+
+///////////////////////////////////////////////////////////////////////////////
+// Writes user specified parameters from options object to outStr
+template <typename TStream>
+void _writeSpecifiedParams(StellarOptions const & options, TStream & outStr)
+{
+//IOREV _notio_
+    // Output user specified parameters
+    outStr << "User specified parameters:" << std::endl;
+    outStr << "  minimal match length             : " << options.minLength << std::endl;
+    outStr << "  maximal error rate (epsilon)     : " << options.epsilon << std::endl;
+    outStr << "  maximal x-drop                   : " << options.xDrop << std::endl;
+    if (options.qGram != std::numeric_limits<size_t>::max())
+        outStr << "  k-mer (q-gram) length            : " << options.qGram << std::endl;
+    outStr << "  search forward strand            : " << ((options.forward) ? "yes" : "no") << std::endl;
+    outStr << "  search reverse complement        : " << ((options.reverse) ? "yes" : "no") << std::endl;
+    outStr << std::endl;
+
+    outStr << "  verification strategy            : " << to_string(options.verificationMethod) << std::endl;
+    if (options.disableThresh != std::numeric_limits<size_t>::max())
+    {
+        outStr << "  disable queries with more than   : " << options.disableThresh << " matches" << std::endl;
+    }
+    outStr << "  maximal number of matches        : " << options.numMatches << std::endl;
+    outStr << "  duplicate removal every          : " << options.compactThresh << std::endl;
+    if (options.maxRepeatPeriod != 1 || options.minRepeatLength != 1000)
+    {
+        outStr << "  max low complexity repeat period : " << options.maxRepeatPeriod << std::endl;
+        outStr << "  min low complexity repeat length : " << options.minRepeatLength << std::endl;
+    }
+    if (options.qgramAbundanceCut != 1)
+    {
+        outStr << "  q-gram abundance cut ratio       : " << options.qgramAbundanceCut << std::endl;
+    }
+
+    outStr << std::endl;
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// Calculates parameters from parameters in options object and writes them to outStr
+// Sets options.qGram if not set by user input
+template <typename TStream>
+void _writeCalculatedParams(StellarOptions & options, TStream & outStr)
+{
+//IOREV _notio_
+    StellarStatistics statistics{options};
+
+    outStr << "Calculated parameters:" << std::endl;
+    if (statistics.kMerComputed)
+    {
+        options.qGram = (unsigned)statistics.kMerLength;
+        outStr << "  k-mer length : " << statistics.kMerLength << std::endl;
+    }
+
+    outStr << "  s^min        : " << statistics.smin << std::endl;
+    outStr << "  threshold    : " << statistics.threshold << std::endl;
+    outStr << "  distance cut : " << statistics.distanceCut << std::endl;
+    outStr << "  delta        : " << statistics.delta << std::endl;
+    outStr << "  overlap      : " << statistics.overlap << std::endl;
+    outStr << std::endl;
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// Writes file name from options object to outStr
+template <typename TStream>
+void _writeFileNames(StellarOptions const & options, TStream & outStr)
+{
+//IOREV _notio_
+    outStr << "I/O options:" << std::endl;
+    outStr << "  database file   : " << options.databaseFile << std::endl;
+    outStr << "  query file      : " << options.queryFile << std::endl;
+    outStr << "  alphabet        : " << options.alphabet << std::endl;
+    outStr << "  output file     : " << options.outputFile << std::endl;
+    outStr << "  output format   : " << options.outputFormat << std::endl;
+    if (options.disableThresh != std::numeric_limits<size_t>::max())
+    {
+        outStr << "  disabled queries: " << options.disabledQueriesFile << std::endl;
+    }
+    outStr << std::endl;
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// Calculates parameters from parameters in options object and from sequences and writes them to outStr
+template <typename sequence_t, typename TStream>
+void _writeMoreCalculatedParams(StellarOptions const & options,
+                                uint64_t const & refLen,
+                                std::vector<sequence_t> const & queries,
+                                TStream & outStr)
+{
+    if (options.qgramAbundanceCut != 1)
+    {
+        outStr << "Calculated parameters:" << std::endl;
+    }
+
+    uint64_t queryLength{0};
+    for (auto & query : queries)
+        queryLength += query.size();
+
+    if (options.qgramAbundanceCut != 1)
+    {
+        outStr << "  q-gram expected abundance : ";
+        outStr << queryLength / (double)((long)1 << (options.qGram << 1)) << std::endl;
+        outStr << "  q-gram abundance threshold: ";
+        outStr << _max(100, (int)(queryLength * options.qgramAbundanceCut)) << std::endl;
+        outStr << std::endl;
+    }
+}
+
+template <typename TStream>
+void _printStellarKernelStatistics(StellarComputeStatistics const & statistics, TStream & outStr)
+{
+    if (statistics.numSwiftHits == 0)
+        return;
+
+    outStr << std::endl << "    # SWIFT hits      : " << statistics.numSwiftHits;
+    outStr << std::endl << "    Longest hit       : " << statistics.maxLength;
+    outStr << std::endl << "    Avg hit length    : " << statistics.totalLength/statistics.numSwiftHits;
+}
+
+template <typename TStream>
+void _printDatabaseIdAndStellarKernelStatistics(
+    bool const verbose,
+    bool const databaseStrand,
+    CharString const & databaseID,
+    StellarComputeStatistics const & statistics,
+    TStream & outStr)
+{
+    outStr << "  " << databaseID;
+    if (!databaseStrand)
+        outStr << ", complement";
+    outStr << std::flush;
+
+    if (verbose)
+    {
+        _printStellarKernelStatistics(statistics, outStr);
+    }
+    outStr << std::endl;
+}
+
+template <typename TStream>
+void _printStellarStatistics(
+        bool const verbose,
+        bool const databaseStrand,
+        StringSet<CharString> const & databaseIDs,
+        StellarComputeStatisticsCollection const & computeStatistics,
+        TStream & outStr)
+{
+    std::cerr << std::endl; // swift filter output is on same line
+    for (size_t i = 0; i < length(databaseIDs); ++i)
+    {
+        CharString const & databaseID = databaseIDs[i];
+        StellarComputeStatistics const & statistics = computeStatistics[i];
+        _printDatabaseIdAndStellarKernelStatistics(verbose, databaseStrand, databaseID, statistics, outStr);
+    }
+}
+
+template <typename TStream>
+void _writeOutputStatistics(StellarOutputStatistics const & statistics,
+                            bool const verbose,
+                            bool const writeDisabledQueriesFile,
+                            TStream & outStr)
+{
+    outStr << "# Eps-matches     : " << statistics.numMatches << std::endl;
+    if (verbose) {
+        if (statistics.numMatches > 0) {
+            outStr << "Longest eps-match : " << statistics.maxLength << std::endl;
+            outStr << "Avg match length  : " << statistics.totalLength / statistics.numMatches << std::endl;
+        }
+        if (writeDisabledQueriesFile)
+            outStr << "# Disabled queries: " << statistics.numDisabled << std::endl;
+    }
+}
+
+} // namespace dream_stellar