added a flag to indicate if a filter requires

variant classification
gkno · May 4, 2014 · 2341939 · 2341939
1 parent 3730136
commit 2341939
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/filter.cpp b/filter.cpp
@@ -604,6 +604,7 @@ Filter::Filter(std::string exp, VariantManip *vm)
  */
 void Filter::parse(const char* exp, bool debug)
 {
+    need_to_classify_variant = false;
     if (strlen(exp)!=0)
     {
         if (tree!=NULL)
@@ -713,9 +714,6 @@ void Filter::parse(const char* exp, int32_t len, Node *node, bool debug)
 
         node->type = type;
 
-        need_to_classif_variant = true;
-
-
         node->left = new Node();
         parse(exp, p-exp+1, node->left, debug);
 
@@ -796,6 +794,7 @@ void Filter::parse_literal(const char* exp, int32_t len, Node * node, bool debug
     }
     else if (strncmp(exp, "VTYPE", 5)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_VARIANT_TYPE;
         if (debug) std::cerr << "\tis variant_op\n";
         return;
@@ -808,40 +807,46 @@ void Filter::parse_literal(const char* exp, int32_t len, Node * node, bool debug
     }
     else if (strncmp(exp, "INDEL", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_INT;
         node->i = VT_INDEL;
         if (debug) std::cerr << "\tis INDEL\n";
         return;
     }
     else if (strncmp(exp, "SNP", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_INT;
         node->i = VT_SNP;
         if (debug) std::cerr << "\tis SNP\n";
         return;
     }
     else if (strncmp(exp, "MNP", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_INT;
         node->i = VT_MNP;
         if (debug) std::cerr << "\tis MNP\n";
         return;
     }
     else if (strncmp(exp, "CLUMPED", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_INT;
         node->i = VT_CLUMPED;
         if (debug) std::cerr << "\tis CLUMPED\n";
         return;
     }
     else if (strncmp(exp, "DLEN", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_VARIANT_DLEN;
         if (debug) std::cerr << "\tis dlen\n";
         return;
     }
     else if (strncmp(exp, "LEN", len)==0)
     {
+        need_to_classify_variant = true;
         node->type = VT_VARIANT_LEN;
         if (debug) std::cerr << "\tis len\n";
         return;

diff --git a/filter.h b/filter.h
@@ -119,7 +119,7 @@ class Filter
     bcf_hdr_t *h;
     bcf1_t *v;
     Variant *variant;
-    bool need_to_classif_variant;
+    bool need_to_classify_variant;
 
     /**
      * Constructor.

diff --git a/variant_manip.h b/variant_manip.h
@@ -77,7 +77,7 @@ class Allele
     int32_t tv;    //no. of tranversions (mlen-ts)
     int32_t ins;   //no. of insertions 
     int32_t del;   //no. of deletions 
-
+    
     Allele(int32_t type, int32_t diff, int32_t alen, int32_t dlen, int32_t tlen, int32_t mlen, int32_t ts)
     {
         this->type = type;
@@ -136,7 +136,7 @@ class Variant
     int32_t mlen;    //motif length
     int32_t tlen;    //reference tract length
     std::vector<Allele> alleles;
-
+    
     Variant()
     {
         type = VT_REF;