bit-score cleanup

Author: h-2

src/search_algo.hpp

@@ -1736,7 +1736,7 @@ computeBlastMatch(typename TBlastRecord::TBlastMatch  & bm,
     computeBitScore(bm, context(lH.gH.outfile));
 
     computeEValueThreadSafe(bm, record.qLength, context(lH.gH.outfile));
-    if (bm.eValue > lH.options.eCutOff)
+    if (bm.eValue > lH.options.maxEValue)
         return EVALUE;
 
     _setFrames(bm, m, lH);
@@ -2431,9 +2431,9 @@ iterateMatchesFullSimd(TLocalHolder & lH)
     {
         TBlastMatch & bm = *it;
 
-        if (lH.options.minBitScore >= 0)
+        if (lH.options.minBitScore > 0)
         {
-            seqan::computeBitScore(bm, seqan::context(lH.gH.outfileBlastTab));
+            seqan::computeBitScore(bm, seqan::context(lH.gH.outfile));
 
             if (bm.bitScore < lH.options.minBitScore)
             {
@@ -2443,9 +2443,9 @@ iterateMatchesFullSimd(TLocalHolder & lH)
             }
         }
 
-        if (lH.options.maxEValue >= 0)
+        if (lH.options.maxEValue < 100)
         {
-            computeEValueThreadSafe(bm, bm.qLength, seqan::context(lH.gH.outfileBlastTab));
+            computeEValueThreadSafe(bm, bm.qLength, seqan::context(lH.gH.outfile));
 
             if (bm.eValue > lH.options.maxEValue)
             {
@@ -2496,11 +2496,11 @@ iterateMatchesFullSimd(TLocalHolder & lH)
         }
 
         // not computed previously
-        if (lH.options.minBitScore < 0)
-            seqan::computeBitScore(bm, seqan::context(lH.gH.outfileBlastTab));
+        if (lH.options.minBitScore == 0)
+            seqan::computeBitScore(bm, seqan::context(lH.gH.outfile));
 
-        if (lH.options.maxEValue < 0)
-            computeEValueThreadSafe(bm, bm.qLength, seqan::context(lH.gH.outfileBlastTab));
+        if (lH.options.maxEValue == 100)
+            computeEValueThreadSafe(bm, bm.qLength, seqan::context(lH.gH.outfile));
 
         ++it;
     }
@@ -2611,9 +2611,16 @@ iterateMatchesFullSerial(TLocalHolder & lH)
                                                            -band,
                                                            +band);
 
-        computeEValueThreadSafe(bm, record.qLength, context(lH.gH.outfile));
+        computeBitScore(bm, context(lH.gH.outfile));
+        if (bm.bitScore < lH.options.minBitScore)
+        {
+            ++lH.stats.hitsFailedExtendBitScoreTest;
+            record.matches.pop_back();
+            continue;
+        }
 
-        if (bm.eValue > lH.options.eCutOff)
+        computeEValueThreadSafe(bm, record.qLength, context(lH.gH.outfile));
+        if (bm.eValue > lH.options.maxEValue)
         {
             ++lH.stats.hitsFailedExtendEValueTest;
             record.matches.pop_back();
@@ -2638,7 +2645,6 @@ iterateMatchesFullSerial(TLocalHolder & lH)
             continue;
         }
 
-        computeBitScore(bm, context(lH.gH.outfile));
 
         if (lH.options.hasSTaxIds)
             bm.sTaxIds = lH.gH.sTaxIds[bm._n_sId];

src/search_options.hpp

@@ -95,7 +95,8 @@ struct LambdaOptions : public SharedOptions
     int             misMatch        = 0; // only for manual
 
     int             xDropOff    = 0;
-    int32_t         minBitScore = -1;
+    int             band        = -1;
+    double          minBitScore = 0;
     double          maxEValue   = 1e-04;
     int             idCutOff    = 0;
     unsigned long   maxMatches  = 500;
@@ -247,6 +248,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
     setMinValue(parser, "e-value", "0");
     setMaxValue(parser, "e-value", "100");
 
+    addOption(parser, ArgParseOption("", "bit-score",
+        "Output only matches that score above this threshold.",
+        ArgParseArgument::DOUBLE));
+    setDefaultValue(parser, "bit-score", "0");
+    setMinValue(parser, "bit-score", "0");
+    setMaxValue(parser, "bit-score", "1000");
+
+
     addOption(parser, ArgParseOption("n", "num-matches",
         "Print at most this number of matches per query.",
         ArgParseArgument::INTEGER));
@@ -771,7 +780,8 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
 
     getOptionValue(options.seedDeltaIncreasesLength, parser, "seed-delta-increases-length");
 
-    getOptionValue(options.eCutOff, parser, "e-value");
+    getOptionValue(options.maxEValue, parser, "e-value");
+    getOptionValue(options.minBitScore, parser, "bit-score");
     getOptionValue(options.idCutOff, parser, "percent-identity");
 
     getOptionValue(options.xDropOff, parser, "x-drop");