From 5dd64f6d204f894967f3a998adf4659326265e35 Mon Sep 17 00:00:00 2001
From: Michael Schatz <mschatz@github.com>
Date: Fri, 27 Oct 2017 18:30:31 -0400
Subject: [PATCH] prioritize sniffles variants over others

---
 src/scrubvcf.pl | 93 ++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 76 insertions(+), 17 deletions(-)

diff --git a/src/scrubvcf.pl b/src/scrubvcf.pl
index 68e9a6d..5ee4816 100755
--- a/src/scrubvcf.pl
+++ b/src/scrubvcf.pl
@@ -36,7 +36,7 @@
   {
     $STRIP_OVERLAP = 1;
     shift @ARGV;
-    my $gender = shift @ARGV;
+    my $gender = shift @ARGV or die "Must specific a gender (male or female) when stripping overlapping variants\n";
     print STDERR "stripping overlapping calls (gender = $gender)\n";
 
     if    ($gender eq "male")   { }  ## nothing to do 
@@ -51,8 +51,9 @@
 
 my $lastchr = undef;
 
-my $lastpos0 = -1; my $lastref0 = ""; my $lastalt0 = "";
-my $lastpos1 = -1; my $lastref1 = ""; my $lastalt1 = "";
+my $lastpos0 = -1; my $lastref0 = ""; my $lastalt0 = ""; my $lastline0 = undef; my $lastsniffles0 = 0; 
+my $lastpos1 = -1; my $lastref1 = ""; my $lastalt1 = ""; my $lastline1 = undef; my $lastsniffles1 = 0;
+my $lasthomo = 0;
 
 while (<>)
 {
@@ -69,6 +70,7 @@
     my $alt      = $fields[4];
     my $qual     = $fields[5];
     my $filter   = $fields[6];
+    my $info     = $fields[7];
     my $genotype = (split (/:/, $fields[9]))[0];
 
     if ($STRIP_OVERLAP)
@@ -85,6 +87,21 @@
         next;
       }
 
+      ## see if we can print the last variants because we have moved to a different chromosome or moved passed them
+      if (defined $lastchr)
+      {
+        if ($lastchr ne $chr)
+        {
+          if (defined $lastline0) { print $lastline0; $lastline0 = undef; if ($lasthomo) { $lastline1 = undef; }}
+          if (defined $lastline1) { print $lastline1; $lastline1 = undef; }
+        }
+        else
+        {
+          if ((defined $lastline0) && ($pos > $lastpos0)) { print $lastline0; $lastline0 = undef; if ($lasthomo) { $lastline1 = undef; } }
+          if ((defined $lastline1) && ($pos > $lastpos1)) { print $lastline1; $lastline1 = undef; }
+        }
+      }
+
       my $printvar = 1;
 
       my $type = "SUB";
@@ -95,33 +112,71 @@
       if    ($genotype eq "0|1") { $hap = 1; }
       elsif ($genotype eq "1|0") { $hap = 0; }
 
+      my $issniffles = 0;
+      if (index($info, "Sniffles") >= 0) { $issniffles = 1; }
+
       if ((defined $lastchr) && ($chr eq $lastchr))
       {
-        if (($hap == 0) || ($hap == 2)) { if ($pos <= $lastpos0) 
-        { $printvar = 0; $types{"FAIL_$hap"}++; print STDERR " overlap detected on hap $hap (lastpos: $lastpos0 $lastref0 $lastalt0) at $_"; } }
+        if (($hap == 0) || ($hap == 2)) 
+        { 
+          if ($pos <= $lastpos0) 
+          { 
+            if ($issniffles && !$lastsniffles0)
+            {
+               ## rescued
+               $types{"OVERRULE_$hap"}++;
+               $lastline0 = undef; if ($lasthomo) { $lastline1 = undef; $lastpos1 = -1; }
+               print STDERR " overrule overlap detected on hap $hap (lastpos: $lastpos0 $lastref0 $lastalt0) at $_"; 
+            }
+            else
+            {
+              $printvar = 0; 
+              $types{"FAIL_$hap"}++; 
+              if ($issniffles) { $types{"FAIL_SNIFFLES_$hap"}++; }
+              print STDERR " overlap detected on hap $hap (lastpos: $lastpos0 $lastref0 $lastalt0) at $_"; 
+            } 
+          }
+        }
 
-        if (($hap == 1) || ($hap == 2)) { if ($pos <= $lastpos1) 
-        { $printvar = 0; $types{"FAIL_$hap"}++; print STDERR " overlap detected on hap $hap (lastpos: $lastpos1 $lastref1 $lastalt1) at $_"; } }
+        if ($printvar)
+        {
+          if (($hap == 1) || ($hap == 2)) 
+          { 
+            if ($pos <= $lastpos1) 
+            { 
+              if ($issniffles && !$lastsniffles1)
+              {
+                ## rescued
+                $types{"OVERRULE_$hap"}++;
+                $lastline1 = undef; if ($lasthomo) { $lastline0 = undef; $lastpos0 = -1; }
+                print STDERR " overrule overlap detected on hap $hap (lastpos: $lastpos1 $lastref1 $lastalt1) at $_"; 
+              }
+              else
+              {
+                $printvar = 0; 
+                $types{"FAIL_$hap"}++; 
+                if ($issniffles) { $types{"FAIL_SNIFFLES_$hap"}++; }
+                print STDERR " overlap detected on hap $hap (lastpos: $lastpos1 $lastref1 $lastalt1) at $_"; 
+              }
+            } 
+          }
+        }
       } 
 
       if ($printvar)
       {
         $reported++;
         $types{$type}++;
-        print $_;
+        #print $_; ## Dont print right away, since there might be a sniffles SV next
 
-        if ((!defined $lastchr) || ($lastchr ne $chr))
-        {
-          # reset the chromosome
-          $lastchr = $chr;
-          $lastpos0 = -1; $lastref0 = ""; $lastalt0 = "";
-          $lastpos1 = -1; $lastref1 = ""; $lastalt1 = "";
-        }
+        $lastchr = $chr;
 
         my $newpos = $pos + length($ref) - 1;
 
-        if (($hap == 0) || ($hap == 2)) { $lastpos0 = $newpos; $lastref0 = $ref; $lastalt0 = $alt; }
-        if (($hap == 1) || ($hap == 2)) { $lastpos1 = $newpos; $lastref1 = $ref; $lastalt1 = $alt; }
+        if (($hap == 0) || ($hap == 2)) { $lastpos0 = $newpos; $lastref0 = $ref; $lastalt0 = $alt; $lastline0 = $_; $lastsniffles0 = $issniffles; }
+        if (($hap == 1) || ($hap == 2)) { $lastpos1 = $newpos; $lastref1 = $ref; $lastalt1 = $alt; $lastline1 = $_; $lastsniffles1 = $issniffles; }
+
+        if ($hap == 2) { $lasthomo = 1; } else { $lasthomo = 0; }
       }
     }
     else
@@ -136,6 +191,10 @@
   }
 }
 
+if (defined $lastline0) { print $lastline0; $lastline0 = undef; if ($lasthomo) { $lastline1 = undef; }}
+if (defined $lastline1) { print $lastline1; $lastline1 = undef; }
+
+
 print STDERR "## Reported $reported of $all variants:\n";
 foreach my $t (sort keys %types)
 {