From e0781a53c2a9a339e9fb4194af8de12a6688ed0a Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell <h2+github.com@fsfe.org>
Date: Fri, 16 Feb 2018 19:56:23 +0100
Subject: [PATCH 1/2] [FIX] prevent breakage with seqan 2.4.0

---
 src/holders.hpp | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/holders.hpp b/src/holders.hpp
index cf0541a38..f51fafe17 100644
--- a/src/holders.hpp
+++ b/src/holders.hpp
@@ -385,7 +385,16 @@ class LocalDataHolder
                             ArrayGaps>;
     using TAlignRow1 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransSubjSeqs>::Type>::Type,
                             ArrayGaps>;
-    using TDPContext = DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>;
+#if (SEQAN_VERSION_MINOR < 4)
+    using TDPContext =  DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>;
+#else
+    using TCellValue  = int16_t;
+    using TDPCell     = DPCell_<TCellValue, TScoreExtension>;
+    using TTraceValue = typename TraceBitMap_<TCellValue>::Type;
+    using TScoreHost  = String<TDPCell, Alloc<OverAligned> >;
+    using TTraceHost  = String<TTraceValue, Alloc<OverAligned> >;
+    using TDPContext  = DPContext<TDPCell, TTraceValue, TScoreHost, TTraceHost>;
+#endif
     using TAliExtContext = AliExtContext_<TAlignRow0, TAlignRow1, TDPContext>;
 
     TAliExtContext      alignContext;

From f38cb0d88e74f182e18347080e1618359f065baf Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell <h2+github.com@fsfe.org>
Date: Fri, 16 Feb 2018 19:56:41 +0100
Subject: [PATCH 2/2] [FIX] silence warning with seqan 2.4.0

---
 src/options.hpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/options.hpp b/src/options.hpp
index b70b56a06..d1e2f4fd3 100644
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -420,14 +420,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
         "Query sequences.",
         ArgParseArgument::INPUT_FILE,
         "IN"));
-    setValidValues(parser, "query", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+    setValidValues(parser, "query", getFileExtensions(SeqFileIn()));
     setRequired(parser, "q");
 
     addOption(parser, ArgParseOption("d", "database",
         "Path to original database sequences (a precomputed index with .sa or .fm needs to exist!).",
         ArgParseArgument::INPUT_FILE,
         "IN"));
-    setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+    setValidValues(parser, "database", getFileExtensions(SeqFileIn()));
     setRequired(parser, "d");
 
     addOption(parser, ArgParseOption("di", "db-index-type",
@@ -1048,7 +1048,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)
         ArgParseArgument::INPUT_FILE,
         "IN"));
     setRequired(parser, "database");
-    setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));
+    setValidValues(parser, "database", getFileExtensions(SeqFileIn()));
 
     addOption(parser, ArgParseOption("s",
         "segfile",