[med-svn] [Git][med-team/lambda-align][upstream] New upstream version 1.0.3

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / lambda-align


Commits:
142f48e4 by Michael R. Crusoe at 2018-02-17T09:30:44-08:00
New upstream version 1.0.3
- - - - -


2 changed files:

- src/holders.hpp
- src/options.hpp


Changes:

=====================================
src/holders.hpp
=====================================
--- a/src/holders.hpp
+++ b/src/holders.hpp
@@ -385,7 +385,16 @@ public:
                             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;


=====================================
src/options.hpp
=====================================
--- 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",



View it on GitLab: https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e

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View it on GitLab: https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e
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