Fix problems with -E cis_splice_effects

griffithlab · May 18, 2017 · c3a0c09 · c3a0c09
1 parent 7a332b1
commit c3a0c09
Show file tree

Hide file tree

Showing 2 changed files with 50 additions and 0 deletions.
diff --git a/src/variants/variants_annotator.cc b/src/variants/variants_annotator.cc
@@ -193,6 +193,22 @@ void VariantsAnnotator::set_variant_cis_effect_limits_ps(const vector<BED>& exon
     return;
 }
 
+//Set limits on + strand for exonic/intronic case
+inline
+void VariantsAnnotator::set_variant_cis_effect_limits_exonic_intronic_ps(const vector<BED>& exons,
+                                                      AnnotatedVariant& variant) {
+    variant.cis_effect_start = exons[0].start;
+    variant.cis_effect_end = exons[exons.size() - 1].end;
+}
+
+//Set limits on - strand for exonic/intronic case
+inline
+void VariantsAnnotator::set_variant_cis_effect_limits_exonic_intronic_ns(const vector<BED>& exons,
+                                                      AnnotatedVariant& variant) {
+    variant.cis_effect_end = exons[0].end;
+    variant.cis_effect_start = exons[exons.size() - 1].start;
+}
+
 //Set limits on - strand
 inline
 void VariantsAnnotator::set_variant_cis_effect_limits_ns(const vector<BED>& exons,
@@ -241,6 +257,27 @@ void VariantsAnnotator::set_variant_cis_effect_limits(const vector<BED>& exons,
     }
 }
 
+//Get the coordinates which limit the effect of this variant.
+//The cis-splice-effects command uses these fields to pull out
+//junctions which might be related to the presence of this variant.
+//This is set to the nearest acceptor and donor of the neigboring
+//exons. The calculation will vary according to the strand of this
+//transcript.
+//This is for exonic/intronic variants - not necessarily in the splice region
+inline
+void VariantsAnnotator::set_variant_cis_effect_limits_exonic_intronic(const vector<BED>& exons,
+                                                      AnnotatedVariant& variant) {
+    string transcript_strand = exons[0].strand;
+    if(transcript_strand == "+") {
+        set_variant_cis_effect_limits_exonic_intronic_ps(exons, variant);
+        return;
+    }
+    if(transcript_strand == "-") {
+        set_variant_cis_effect_limits_exonic_intronic_ns(exons, variant);
+        return;
+    }
+}
+
 //Overlap splice region in the negative strand
 void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>& exons,
                                                       AnnotatedVariant& variant) {
@@ -258,6 +295,7 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "exonic";
+                set_variant_cis_effect_limits_exonic_intronic(exons, variant);
                 return;
             }
         }
@@ -267,6 +305,7 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
                 variant.score =  common::num_to_str(min(variant.end - exons[i+1].end,
                                                         exons[i].start - variant.end));
                 variant.annotation = "intronic";
+                set_variant_cis_effect_limits_exonic_intronic(exons, variant);
                 return;
             }
         }
@@ -341,6 +380,7 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "exonic";
+                set_variant_cis_effect_limits_exonic_intronic(exons, variant);
                 return;
             }
         }
@@ -351,6 +391,7 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
                 variant.score =  common::num_to_str(min(variant.end - exons[i].end,
                                                         exons[i+1].start - variant.end));
                 variant.annotation = "intronic";
+                set_variant_cis_effect_limits_exonic_intronic(exons, variant);
                 return;
             }
         }

diff --git a/src/variants/variants_annotator.h b/src/variants/variants_annotator.h
@@ -221,6 +221,15 @@ class VariantsAnnotator {
         void set_variant_cis_effect_limits_ps(const vector<BED>& exons,
                                               AnnotatedVariant& variant1,
                                               uint32_t i);
+        //Cis limits for exonic/intronic case - figure out strand here
+        void set_variant_cis_effect_limits_exonic_intronic(const vector<BED>& exons,
+                                                              AnnotatedVariant& variant);
+        //Cis limits for exonic/intronic case - negative strand
+        void set_variant_cis_effect_limits_exonic_intronic_ns(const vector<BED>& exons,
+                                                              AnnotatedVariant& variant);
+        //Cis limits for exonic/intronic case - positive strand
+        void set_variant_cis_effect_limits_exonic_intronic_ps(const vector<BED>& exons,
+                                                              AnnotatedVariant& variant);
 };
 
 inline string variant_set_to_string(const set<AnnotatedVariant> &av1) {