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Cleanup comments

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commit ed45ad65d1748fa43eaf4dbfaaf599a6c42524ad 1 parent ddee4c7
@jts authored
Showing with 0 additions and 32 deletions.
  1. +0 −32 src/StringGraph/SGVisitors.cpp
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32 src/StringGraph/SGVisitors.cpp
@@ -67,8 +67,6 @@ bool SGTransitiveReductionVisitor::visit(StringGraph* /*pGraph*/, Vertex* pVerte
Edge* pVWEdge = edges[i];
Vertex* pWVert = pVWEdge->getEnd();
- //std::cout << "Examining edges from " << pWVert->getID() << " longest: " << longestLen << "\n";
- //std::cout << pWVert->getID() << " w_edges: \n";
EdgeDir transDir = !pVWEdge->getTwinDir();
if(pWVert->getColor() == GC_GRAY)
{
@@ -83,7 +81,6 @@ bool SGTransitiveReductionVisitor::visit(StringGraph* /*pGraph*/, Vertex* pVerte
{
// X is the endpoint of an edge of V, therefore it is transitive
pWXEdge->getEnd()->setColor(GC_BLACK);
- //std::cout << "Marking " << pWXEdge->getEndID() << " as transitive to " << pVertex->getID() << "\n";
}
}
else
@@ -98,13 +95,10 @@ bool SGTransitiveReductionVisitor::visit(StringGraph* /*pGraph*/, Vertex* pVerte
Edge* pVWEdge = edges[i];
Vertex* pWVert = pVWEdge->getEnd();
- //std::cout << "Examining edges from " << pWVert->getID() << " longest: " << longestLen << "\n";
- //std::cout << pWVert->getID() << " w_edges: \n";
EdgeDir transDir = !pVWEdge->getTwinDir();
EdgePtrVec w_edges = pWVert->getEdges(transDir);
for(size_t j = 0; j < w_edges.size(); ++j)
{
- //std::cout << " edge: " << *w_edges[j] << "\n";
Edge* pWXEdge = w_edges[j];
size_t len = pWXEdge->getSeqLen();
@@ -114,8 +108,6 @@ bool SGTransitiveReductionVisitor::visit(StringGraph* /*pGraph*/, Vertex* pVerte
{
// X is the endpoint of an edge of V, therefore it is transitive
pWXEdge->getEnd()->setColor(GC_BLACK);
- //std::cout << "Marking " << pWXEdge->getEndID() << " as transitive to " << pVertex->getID() << " in stage 2";
- //std::cout << " via " << pWVert->getID() << "\n";
}
}
else
@@ -335,14 +327,6 @@ bool SGTrimVisitor::visit(StringGraph* /*pGraph*/, Vertex* pVertex)
}
}
- /*
- if(isTrimmed)
- {
- std::stringstream ss;
- ss << pVertex->getID() << "-trimmed";
- writeFastaRecord(&m_tmpFile, ss.str(), pVertex->getSeq().toString());
- }
- */
return false;
}
@@ -447,12 +431,6 @@ bool SGSmallRepeatResolveVisitor::visit(StringGraph* /*pGraph*/, Vertex* pX)
if(x_diff > m_minDiff && y_diff > m_minDiff)
{
- /*
- printf("Edge %s -> %s is likely a repeat\n", pX->getID().c_str(), pY->getID().c_str());
- printf("Actual overlap lengths: %zu and %zu\n", xy_len, yx_len);
- printf("Spanned by longer edges of size: %zu and %zu\n", x_longest_len, y_longest_len);
- printf("Differences: %d and %d\n", x_diff, y_diff);
- */
pX->deleteEdge(pXY);
pY->deleteEdge(pYX);
changed = true;
@@ -726,14 +704,6 @@ bool SGSmoothingVisitor::visit(StringGraph* pGraph, Vertex* pVertex)
cigarSS << cigarOp;
}
cigarStrings[i] = cigarSS.str();
-
- /*
- printf("1: %s\n", aln_global->out1);
- printf("M: %s\n", aln_global->outm);
- printf("2: %s\n", aln_global->out2);
- printf("CIGAR: %s\n", cigarStrings[i].c_str());
- */
-
aln_free_AlnAln(aln_global);
}
@@ -752,8 +722,6 @@ bool SGSmoothingVisitor::visit(StringGraph* pGraph, Vertex* pVertex)
gapPercent[i] = percentGap;
totalPercent[i] = percentDiff;
maxIndel[i] = maxGapLength;
-
- //printf("ml: %d tmm: %d pd: %lf pg: %lf\n", matchLen, totalDiff, percentDiff, percentGap);
}
if(bIsDegenerate || bFailGapCheck || bFailDivergenceCheck || bFailIndelSizeCheck)
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