dbsnp missing from indel header. cleaned some code

walaj · Dec 19, 2016 · 5213029 · 5213029
1 parent c90438a
commit 5213029
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Showing 9 changed files with 131 additions and 344 deletions.
diff --git a/src/Snowman/AlignedContig.cpp b/src/Snowman/AlignedContig.cpp
@@ -363,8 +363,6 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) {
 
 	  bp.secondary = a.m_align.SecondaryFlag() || b.m_align.SecondaryFlag();
 
-	  assert(bp.valid());
-
 	  // add the the vector of breakpoints
 	  if (!bp.secondary) {
 	    m_local_breaks.push_back(bp);
@@ -434,7 +432,6 @@ void AlignedContig::blacklist(SeqLib::GRC &grv) {
     // order the breakpoint
     m_global_bp.order();
 
-    assert(m_global_bp.valid());
   }
 
   std::string AlignedContig::printDiscordantClusters() const {

diff --git a/src/Snowman/AlignmentFragment.cpp b/src/Snowman/AlignmentFragment.cpp
@@ -97,7 +97,6 @@ void AlignmentFragment::SetIndels(const AlignedContig * c) {
     while (parseIndelBreak(bp) && fail_safe_count++ < MAX_INDELS && !m_align.SecondaryFlag()) {
       bp.aligned_covered = c->aligned_covered;
       assert(bp.aligned_covered);
-      assert(bp.valid());
       for (auto& i : c->prefixes)
 	bp.allele[i].indel = true;
       m_indel_breaks.push_back(bp);
@@ -290,7 +289,6 @@ void AlignmentFragment::indelCigarMatches(const std::unordered_map<std::string,
     bp.b1.gr.strand = '+';
     bp.b2.gr.strand = '-';
 
-    assert(bp.valid());
     return true;
   }