[FEATURE] large commit finally bringing bidirectional FM

seqan · Oct 13, 2016 · d336238 · d336238
1 parent b63e507
commit d336238
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Showing 6 changed files with 280 additions and 146 deletions.
diff --git a/src/holders.hpp b/src/holders.hpp
@@ -271,7 +271,8 @@ class GlobalDataHolder
     using TMatch         = Match<TRedAlph>;
 
     static constexpr BlastProgram blastProgram  = p;
-    static constexpr bool indexIsFM             = std::is_same<TIndexSpec_, TFMIndex<>>::value;
+    static constexpr bool indexIsBiFM           = std::is_same<TIndexSpec_, BidirectionalIndex<TFMIndex<>>>::value;
+    static constexpr bool indexIsFM             = std::is_same<TIndexSpec_, TFMIndex<>>::value || indexIsBiFM;
     static constexpr bool alphReduction         = !std::is_same<TransAlph<p>, TRedAlph>::value;
 
     /* Sequence storage types */
@@ -354,9 +355,6 @@ class GlobalDataHolder
     TPositions          untransQrySeqLengths;   // used iff qIsTranslated(p)
     TPositions          untransSubjSeqLengths;  // used iff sIsTranslated(p)
 
-    TMasking            segIntStarts;
-    TMasking            segIntEnds;
-
     StatsHolder         stats;
 
     GlobalDataHolder() :

diff --git a/src/lambda.cpp b/src/lambda.cpp
@@ -294,6 +294,13 @@ argConv4(LambdaOptions                        & options,
                                    BlastProgramSelector<p>(),
                                    TRedAlph(),
                                    TScoreExtension());
+    else if (options.dbIndexType == DbIndexType::BI_FM_INDEX)
+        return realMain<BidirectionalIndex<TFMIndex<>>>(options,
+                                                        TOutFormat(),
+                                                        BlastTabularSpecSelector<h>(),
+                                                        BlastProgramSelector<p>(),
+                                                        TRedAlph(),
+                                                        TScoreExtension());
     else
         return realMain<TFMIndex<>>(options,
                                    TOutFormat(),
@@ -352,10 +359,6 @@ realMain(LambdaOptions                        & options,
     if (ret)
         return ret;
 
-//     ret = loadSegintervals(globalHolder, options);
-//     if (ret)
-//         return ret;
-
     ret = loadQuery(globalHolder, options);
     if (ret)
         return ret;