Add option to store discovered adapters and use them in subsequent runs.

porechop/cpp_function_wrappers.py

@@ -21,7 +21,7 @@
 SO_FILE = 'cpp_functions.so'
 SO_FILE_FULL = os.path.join(os.path.dirname(os.path.realpath(__file__)), SO_FILE)
 if not os.path.isfile(SO_FILE_FULL):
-    sys.exit('could not find ' + SO_FILE + ' - please reinstall')
+    sys.exit('could not find ' + SO_FILE_FULL + ' - please reinstall')
 C_LIB = CDLL(SO_FILE_FULL)
 
 C_LIB.adapterAlignment.argtypes = [c_char_p,  # Read sequence

porechop/include/seqan/LICENSE

@@ -0,0 +1,27 @@
+Copyright (c) 2006-2018, Knut Reinert, FU Berlin
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of Knut Reinert or the FU Berlin nor the names of
+      its contributors may be used to endorse or promote products derived
+      from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+

porechop/include/seqan/align.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,6 +53,7 @@
 #include <algorithm>
 
 #include <seqan/basic.h>
+#include <seqan/simd.h>
 #include <seqan/modifier.h>  // ModifiedAlphabet<>.
 #include <seqan/align/align_metafunctions.h>
 #include <seqan/graph_align.h>  // TODO(holtgrew): We should not have to depend on this.
@@ -76,6 +77,8 @@
 
 #include <seqan/align/fragment.h>
 
+#include <seqan/align/aligned_sequence_concept.h>
+
 #include <seqan/align/gaps_base.h>
 #include <seqan/align/gaps_iterator_base.h>
 

porechop/include/seqan/align/align_base.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -476,7 +476,7 @@ detach(Align<TSource, TSpec> & me)
 
 template <typename TFile, typename TSource, typename TSpec>
 inline void
-write(TFile & target,
+_write(TFile & target,
       Align<TSource, TSpec> const & source)
 {
     typedef Align<TSource, TSpec> const TAlign;
@@ -557,6 +557,15 @@ write(TFile & target,
     writeValue(target, '\n');
 }
 
+template <typename TFile, typename TSource, typename TSpec>
+[[deprecated("Old-style I/O. Use stream operator << instead.")]]
+inline void
+write(TFile & target,
+      Align<TSource, TSpec> const & source)
+{
+    _write(target, source);
+}
+
 // ----------------------------------------------------------------------------
 // Function clearClipping()
 // ----------------------------------------------------------------------------
@@ -607,7 +616,7 @@ operator<<(TStream & target,
            Align<TSource, TSpec> const & source)
 {
     typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
-    write(it, source);
+    _write(it, source);
     return target;
 }
 

porechop/include/seqan/align/align_cols.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/align_config.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/align_interface_wrapper.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,14 +58,20 @@ namespace seqan
 // Function _alignWrapperSequential(); Score; StringSet vs. StringSet
 // ----------------------------------------------------------------------------
 
-template <typename TString1, typename TSpec1,
-          typename TString2, typename TSpec2,
+template <typename TSetH,
+          typename TSetV,
           typename TScoreValue, typename TScoreSpec,
           typename TAlignConfig,
-          typename TGapModel>
+          typename TGapModel,
+          std::enable_if_t<And<And<Is<ContainerConcept<TSetH>>,
+                                   Is<ContainerConcept<typename Value<TSetH>::Type>>>,
+                               And<Is<ContainerConcept<TSetV>>,
+                                   Is<ContainerConcept<typename Value<TSetV>::Type>>>
+                               >::VALUE,
+                           int> = 0>
 inline auto
-_alignWrapperSequential(StringSet<TString1, TSpec1> const & stringsH,
-                        StringSet<TString2, TSpec2> const & stringsV,
+_alignWrapperSequential(TSetH const & stringsH,
+                        TSetV const & stringsV,
                         Score<TScoreValue, TScoreSpec> const & scoringScheme,
                         TAlignConfig const & config,
                         TGapModel const & /*gaps*/)
@@ -92,14 +98,20 @@ _alignWrapperSequential(StringSet<TString1, TSpec1> const & stringsH,
 // Function _alignWrapperSequential(); Score; String vs. StringSet
 // ----------------------------------------------------------------------------
 
-template <typename TString1,
-          typename TString2, typename TSpec,
+template <typename TSeqH,
+          typename TSetV,
           typename TScoreValue, typename TScoreSpec,
           typename TAlignConfig,
-          typename TGapModel>
+          typename TGapModel,
+          std::enable_if_t<And<And<Is<ContainerConcept<TSeqH>>,
+                                   Not<Is<ContainerConcept<typename Value<TSeqH>::Type>>>>,
+                               And<Is<ContainerConcept<TSetV>>,
+                                   Is<ContainerConcept<typename Value<TSetV>::Type>>>
+                               >::VALUE,
+                           int> = 0>
 inline auto
-_alignWrapperSequential(TString1 const & stringH,
-                        StringSet<TString2, TSpec> const & stringsV,
+_alignWrapperSequential(TSeqH const & stringH,
+                        TSetV const & stringsV,
                         Score<TScoreValue, TScoreSpec> const & scoringScheme,
                         TAlignConfig const & config,
                         TGapModel const & /*gaps*/)
@@ -125,21 +137,27 @@ _alignWrapperSequential(TString1 const & stringH,
 // Function _alignWrapperSequential(); Gaps
 // ----------------------------------------------------------------------------
 
-template <typename TSequenceH, typename TGapsSpecH, typename TSetSpecH,
-          typename TSequenceV, typename TGapsSpecV, typename TSetSpecV,
+template <typename TSetH,
+          typename TSetV,
           typename TScoreValue, typename TScoreSpec,
           typename TAlignConfig,
-          typename TGapModel>
+          typename TGapModel,
+          std::enable_if_t<And<And<Is<ContainerConcept<TSetH>>,
+                                   Is<AlignedSequenceConcept<typename Value<TSetH>::Type>>>,
+                               And<Is<ContainerConcept<TSetV>>,
+                                   Is<AlignedSequenceConcept<typename Value<TSetV>::Type>>>
+                               >::VALUE,
+                           int> = 0>
 inline auto
-_alignWrapperSequential(StringSet<Gaps<TSequenceH, TGapsSpecH>, TSetSpecH> & gapSeqSetH,
-                        StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV,
+_alignWrapperSequential(TSetH & gapSeqSetH,
+                        TSetV & gapSeqSetV,
                         Score<TScoreValue, TScoreSpec> const & scoringScheme,
                         TAlignConfig const & config,
                         TGapModel const & /*gaps*/)
 
 {
-    typedef typename Size<TSequenceH>::Type TSize;
-    typedef typename Position<TSequenceH>::Type TPosition;
+    typedef typename Size<TSetH>::Type TSize;
+    typedef typename Position<TSetH>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
 
     String<TScoreValue> results;
@@ -167,7 +185,8 @@ _alignWrapperSequential(StringSet<Gaps<TSequenceH, TGapsSpecH>, TSetSpecH> & gap
 template <typename... TArgs>
 inline auto _alignWrapper(TArgs && ...args)
 {
-#ifdef SEQAN_SIMD_ENABLED
+// NOTE(marehr): ume_simd is currently not working, thus falling back to sequential case
+#if defined(SEQAN_SIMD_ENABLED) && !defined(SEQAN_UMESIMD_ENABLED)
     return _alignWrapperSimd(std::forward<TArgs>(args)...);
 #else
     return _alignWrapperSequential(std::forward<TArgs>(args)...);

porechop/include/seqan/align/align_iterator_base.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/align_metafunctions.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/align_traceback.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/aligned_sequence_concept.h

@@ -0,0 +1,65 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_ALIGNED_SEQUENCE_CONCEPT_H_
+#define INCLUDE_SEQAN_ALIGN_ALIGNED_SEQUENCE_CONCEPT_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+SEQAN_CONCEPT_REFINE(AlignedSequenceConcept, (TSequence), (ContainerConcept))
+{
+
+    SEQAN_CONCEPT_USAGE(AlignedSequenceConcept)
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_ALIGN_ALIGNED_SEQUENCE_CONCEPT_H_

porechop/include/seqan/align/alignment_algorithm_tags.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without

porechop/include/seqan/align/alignment_operations.h

@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without