PD-4217 multi-domain tccP BLASTP result is confused with a fusion pro…

…tein
ncbi · May 27, 2022 · c3d11ac · c3d11ac
1 parent 81e11d4
commit c3d11ac
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Showing 3 changed files with 16 additions and 11 deletions.
diff --git a/amr_report.cpp b/amr_report.cpp
@@ -1251,7 +1251,7 @@ struct BlastAlignment : Alignment
   bool sameMatch (const BlastAlignment* other) const
     // Cf. less()
     { ASSERT (other);
-      ASSERT (targetName     == other->targetName);
+      ASSERT (targetName == other->targetName);
       return    targetStart    == other->targetStart
              && targetEnd      == other->targetEnd
              && getCdsStart () == other->getCdsStart ()
@@ -1844,16 +1844,20 @@ struct Batch
              )
           {
             QC_ASSERT (blastAl->parts == prev->parts);
-            QC_ASSERT (blastAl->parts >= 2);
-            QC_ASSERT (blastAl->part > prev->part);
-            if (! fusionMain)
+            if (blastAl->parts < 2)  // multi-domain tccP problem, PD-4217
+              fusionMain = nullptr;
+            else
             {
-              fusionMain = prev;
-              var_cast (fusionMain) -> fusions << fusionMain;
+              QC_ASSERT (blastAl->part > prev->part);
+              if (! fusionMain)
+              {
+                fusionMain = prev;
+                var_cast (fusionMain) -> fusions << fusionMain;
+              }
+              ASSERT (fusionMain);
+              var_cast (fusionMain) -> fusions << blastAl;
+              var_cast (blastAl) -> fusionRedundant = true;
             }
-            ASSERT (fusionMain);
-            var_cast (fusionMain) -> fusions << blastAl;
-            var_cast (blastAl) -> fusionRedundant = true;
           }
           else
             fusionMain = nullptr;

diff --git a/amrfinder.cpp b/amrfinder.cpp
@@ -33,7 +33,8 @@
 *               cat, tail
 *
 * Release changes:
-*   3.10.28 05/11/2022 PD-4169  N-terminus is the same if shorter than 60 aa
+*   3.10.29 05/27/2022 PD-4217  multi-domain tccP BLASTP result is confused with a fusion protein
+*   3.10.28 05/11/2022 PD-4169  CDSs are the same if CDS difference is shorter than 60 aa
 *   3.10.27 05/06/2022 PD-4119  --database_version
 *   3.10.26 05/02/2022 PD-3292  dependence on "ln" is removed
 *   3.10.25 04/29/2022 PD-3292  dependence on "mv", "cp", "cut", "head" and "sort" is removed

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-3.10.28
+3.10.29