Merge pull request #26 from freerkvandijk/master

Fixed bug introduced in previous version
molgenis · Apr 22, 2017 · 0c50874 · 0c50874
2 parents 7d467e1 + 85addf3
commit 0c50874
Showing 1 changed file with 81 additions and 3 deletions.
diff --git a/CoNVaDING.pl b/CoNVaDING.pl
@@ -19,7 +19,7 @@
 print "#######################################\n";
 
 ######CHANGE VERSION PARAMETER IF VERSION IS UPDATED#####
-my $version = "1.2.0";
+my $version = "1.2.1";
 
 ##############################################################################################
 ##############################################################################################
@@ -1584,6 +1584,7 @@ sub createOutputLists{
     my $shapPassCount = 0;
     my $highQualAbberationCount = 0;
     my @chrStarts;
+    my @chrStartsHOM;
     my $abberationCountHOM = 0;
     my $shapPassCountHOM = 0;
     my $highQualAbberationCountHOM = 0;
@@ -1672,16 +1673,93 @@ sub createOutputLists{
             $abberationCount = 0; #Reset $abberationCount to 0
             $shapPassCount = 0;
         }
-
 
+
+        #Perform second iteration to also write Homozygous events to output
+        $target = $arrayRefs[0][$m];
+        $target =~ s/:/\t/g;
+        $target =~ s/-/\t/g;
+        $target =~ s/^23/X/gs;
+        $target =~ s/^24/Y/gs;
+        $target =~ s/^25/MT/gs;
+        $gene = $arrayRefs[1][$m];
+        $vals = $arrayRefs[2][$m];
+        $vals =~ s/&&/\t/g;
+        $abberation = $arrayRefs[3][$m];
+        $quality = $arrayRefs[4][$m];
+        $shap = $arrayRefs[6][$m];
+        @array = split("\t", $target);
+        if ($abberation eq "HOM_DEL" || $abberation eq "HOM_DUP") { #If abberation detected, check next abberation, afterwards write to longlist file
+            my $nextAbberation = $arrayRefs[3][$m+1];
+            my $nextGene = $arrayRefs[1][$m+1];
+            if ($m == $lastTargetIdx){
+                $nextAbberation = "LAST";
+                $nextGene = "LAST";
+            }
+
+            #Extract chr and start position from target
+            my @array = split("\t", $target);
+            $chr = $array[0];
+            $start = $array[1];
+            $stop = $array[2];
+            if ($abberationCountHOM == 0) {
+                #$outputLongToWrite .= "$chr\t$start\t"; #Write event chr and start
+            }
+            push(@chrStartsHOM, $chr);
+            push(@chrStartsHOM, $start);
+            if ($quality eq ".") { #If abberation is not filtered out due to low quality autoVC or failing gene low quality, push into shortlist
+                $highQualAbberationCountHOM++; #Increase number of high quality abberation counts
+            }
+            #Count number of targets passing shapiro-wilk test
+            if ($shap >= 0.05){
+                $shapPassCountHOM++;
+            }
+
+            if ($abberation eq $nextAbberation && $gene eq $nextGene){ #If next abberation is DEL or DUP within same gene, same event extended
+                $abberationCountHOM++;
+            }else { #Not the same event anymore, write away stop position, gene and abberation
+                my $abberationCountToPrint = ($abberationCountHOM+1);
+
+                #Retrieve first start to print for event
+                $target = $arrayRefs[0][$m-$abberationCountHOM];
+                $target =~ s/:/\t/g;
+                $target =~ s/-/\t/g;
+                $target =~ s/^23/X/gs;
+                $target =~ s/^24/Y/gs;
+                $target =~ s/^25/MT/gs;
+                #Extract chr and start position from target
+                my @arrayP = split("\t", $target);
+                my $chrP = $arrayP[0];
+                my $startP = $arrayP[1];
+                #$outputLongToWrite .= "$chr\t$start\t$stop\t$gene\t$abberationCountToPrint\t$shapPassCountHOM\t$abberation\n"; #Write event end and details away
+                if ($highQualAbberationCountHOM > 0) { #If total abberation counts is equal to high quality calls all target of an abberation are PASS, so the event can be written to the shortlist
+                    if ($abberationCountHOM == 0 ) {
+                        #$outputShortToWrite .= "$chr\t$start"; #Write event chr and start
+                    }else{
+                        #push(@chrStarts, $chr);
+                        #push(@chrStarts, $start);
+                        #$outputShortToWrite .= $chrStarts[0] . "\t" . $chrStarts[1];
+                    }
+                    $outputShortToWrite .= "$chrP\t$startP\t$stop\t$gene\t$abberationCountToPrint\t$shapPassCountHOM\t$abberation\n"; #Write high quality events
+                }
+                $abberationCountHOM = 0; #Reset $abberationCount to 0
+                $shapPassCountHOM = 0;
+                $highQualAbberationCountHOM = 0; #Reset $highQualAbberationCount to 0
+                undef(@chrStartsHOM); undef($chr); undef($start); undef($stop);
+            }
+        }else{
+            #Undef chr, start array and variables
+            undef(@chrStartsHOM); undef($chr); undef($start); undef($stop);
+            $abberationCountHOM = 0; #Reset $abberationCount to 0
+            $shapPassCountHOM = 0;
+        }
     }
     writeOutput($outputfileTotal, $outputTotalToWrite); #Write output to above specified file
     writeOutput($outputfileLong, $outputLongToWrite); #Write output to above specified file
     writeOutput($outputfileShort, $outputShortToWrite); #Write output to above specified file
     undef(@arrayRefs); undef($outputTotalToWrite); undef($outputLongToWrite); undef($outputShortToWrite);
     undef(%geneCounts);
     undef(%totalGeneCounts);
-
 }
 
 sub allTargetNormalization {