works with two adjacent inversios

baoxingsong · Apr 16, 2024 · 9e1331d · 9e1331d
1 parent b1afd05
commit 9e1331d
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/src/impl/geneSyntenic.cpp b/src/impl/geneSyntenic.cpp
@@ -273,7 +273,7 @@ void longestPath(std::vector<AlignmentMatch> &pairedSimilarFragments, std::vecto
                     prev[idx] = jdx;
                 } else if (pairedSimilarFragments[jdx].getStrand() == NEGATIVE && pairedSimilarFragments[idx].getStrand() == NEGATIVE
                            && pairedSimilarFragments[jdx].getRefEndPos() < pairedSimilarFragments[idx].getRefStartPos()
-                           && pairedSimilarFragments[jdx].getQueryEndPos() < pairedSimilarFragments[idx].getQueryStartPos() && scoreArray[jdx] > scoreThreshold) { // this block is under test, todo remind PHG guies
+                           && pairedSimilarFragments[jdx].getQueryEndPos() < pairedSimilarFragments[idx].getQueryStartPos() && scoreArray[jdx] > scoreThreshold) { // this block is under test, TODO vice versa for two positive strand blocks
                     scoreArray[idx] = scoreArray[jdx] + pairedSimilarFragments[idx].getScore();
                     prev[idx] = jdx;
                 } else if (pairedSimilarFragments[jdx].getStrand() != pairedSimilarFragments[idx].getStrand()

diff --git a/src/service/TransferGffWithNucmerResult.cpp b/src/service/TransferGffWithNucmerResult.cpp
@@ -862,7 +862,9 @@ void setupAnchorsWithSpliceAlignmentResult(const std::string &gffFilePath, const
                             delete [] query_seq_array;
                         }
                     }
-                } else if (lastStrand == NEGATIVE && alignmentMatch.getStrand() == NEGATIVE) {
+                } else if (lastStrand == NEGATIVE && alignmentMatch.getStrand() == NEGATIVE
+                           && alignmentMatch.getRefStartPos() > temp[m-1].getRefEndPos()
+                           && alignmentMatch.getQueryEndPos() < temp[m-1].getQueryStartPos()   ) {
                     if (alignmentMatch.getRefStartPos() == startRef && alignmentMatch.getQueryEndPos() != startQuery) {
 
                     } else if (alignmentMatch.getRefStartPos() != startRef && alignmentMatch.getQueryEndPos() == startQuery) {

diff --git a/src/version.h b/src/version.h
@@ -4,5 +4,5 @@
 
 #pragma once
 
-#define VERSION "1.2.3"
+#define VERSION "1.2.4"
 #define PROGRAMNAME "anchorwave"