Merge pull request #31 from ruolin/exp_filter

Exp filter
ruolin · Apr 3, 2019 · 61a37d3 · 61a37d3
2 parents 17c5ab3 + ee973d4
commit 61a37d3
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,10 +5,10 @@ set( CMAKE_CXX_STANDARD 14 )
 set(CMAKE_BUILD_TYPE Release)
 #set(CMAKE_BUILD_TYPE Debug)
 
-set(CPACK_PACKAGE_VERSION "1.0.3")
+set(CPACK_PACKAGE_VERSION "1.0.5")
 set(CPACK_PACKAGE_VERSION_MAJOR "1")
 set(CPACK_PACKAGE_VERSION_MINOR "0")
-set(CPACK_PACKAGE_VERSION_PATCH "3")
+set(CPACK_PACKAGE_VERSION_PATCH "5")
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
 set(CPACK_PACKAGE_VENDOR "Iowa State University")

diff --git a/include/StrawberryConfig.hpp b/include/StrawberryConfig.hpp
@@ -11,8 +11,8 @@
 namespace strawberry{
    constexpr char majorVersion[] = "1";
    constexpr char minorVersion[] = "0";
-   constexpr char patchVersion[] = "3";
-   constexpr char version[] = "1.0.3";
+   constexpr char patchVersion[] = "5";
+   constexpr char version[] = "1.0.5";
 }
 
 

diff --git a/src/alignments.cpp b/src/alignments.cpp
@@ -1033,7 +1033,7 @@ int Sample::addRef2Cluster(HitCluster &cluster_out){
       size_t mark_next_gene = _refmRNA_offset;
       //continue search a few forward
       int over = 0;
-      while (++_refmRNA_offset < _ref_mRNAs.size() && over++ < 10) {
+      while (++_refmRNA_offset < _ref_mRNAs.size() && over++ < 100) {
          if (_ref_mRNAs[_refmRNA_offset].parent_id() == cluster_out.gene_id()) {
             cluster_out.addRefContig(_ref_mRNAs[_refmRNA_offset]);
          }
@@ -1425,6 +1425,7 @@ vector<Contig> Sample::assembleCluster(const RefSeqTable &ref_t, shared_ptr<HitC
       uint cluster_left = std::numeric_limits<uint>::max();
       vector<Contig> hits;
       uint cluster_right = 0;
+      assert(!cluster->_ref_mRNAs.empty());
       for (const auto& i: cluster->_ref_mRNAs) {
          cluster_left = min(cluster_left, i.left());
          cluster_right = max(cluster_right, i.right());
@@ -1446,7 +1447,7 @@ vector<Contig> Sample::assembleCluster(const RefSeqTable &ref_t, shared_ptr<HitC
       int tid=0;
       for (Contig& asmb: assembled_transcripts) {
          ++tid;
-         asmb.parent_id() = "gene."+to_string(cluster->_id);
+         asmb.parent_id() = cluster->_ref_mRNAs[0].parent_id();
          asmb.annotated_trans_id("transcript." + to_string(cluster->_id) + "." + to_string(tid));
       }
       this->fragLenDist(ref_t, assembled_transcripts, cluster, plogfile);
@@ -1733,7 +1734,6 @@ void Sample::procSample(FILE *pfile, FILE *plogfile, FILE *fragfile)
       pretty_print(fragfile, header, "\t");
    }
 
-
    while(true){
      //++_num_cluster;
      shared_ptr<HitCluster> cluster (new HitCluster());
@@ -1786,8 +1786,8 @@ void Sample::procSample(FILE *pfile, FILE *plogfile, FILE *fragfile)
        isoforms.insert(isoforms.end(), iso.begin(), iso.end());
      }
 #else
-     finalizeCluster(last_cluster, true);
-     auto iso = this->quantifyCluster(ref_t, last_cluster, transcripts, pfile, plogfile);
+     finalizeCluster(cluster, true);
+     auto iso = this->quantifyCluster(ref_t, cluster, cluster->ref_mRNAs(), plogfile, fragfile);
 #endif
    } //end while(true)