From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 14 Apr 2010 15:44:50 +0000 (+0000)
Subject: Speedup with -i, no need to query the reference all the time
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=316dda05588353f7640d0713e470f703d7daf338;p=samtools.git

Speedup with -i, no need to query the reference all the time
---

diff --git a/misc/sam2vcf.pl b/misc/sam2vcf.pl
index 38ab64d..874ad5c 100755
--- a/misc/sam2vcf.pl
+++ b/misc/sam2vcf.pl
@@ -131,7 +131,13 @@ sub do_pileup_to_vcf
         if ( $ref eq '*' )
         {
             # An indel is involved.
-            if ( $ignore_indels ) { next; }
+            if ( $ignore_indels )
+            { 
+                $prev_ref = $ref;
+                $prev_pos = $pos;
+                $prev_chr = $chr;
+                next; 
+            }
 
             if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos) 
             {
@@ -171,7 +177,13 @@ sub do_pileup_to_vcf
         }
         else
         {
-            if ( $ignore_snps ) { next; }
+            if ( $ignore_snps ) 
+            { 
+                $prev_ref = $ref;
+                $prev_pos = $pos;
+                $prev_chr = $chr;
+                next; 
+            }
 
             # SNP
             ($alt,$gt) = iupac_to_gtype($ref,$cons);