X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fexport2sam.pl;h=8e3e2800c3ac82cf9d3d3581b02768ddfd9a16f2;hb=63e8f525a5fd57be4c3471739a3996016e0c25f9;hp=ae82123f9d3a7fd2fdb7a029f55c7200bd8be755;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/misc/export2sam.pl b/misc/export2sam.pl
index ae82123..8e3e280 100755
--- a/misc/export2sam.pl
+++ b/misc/export2sam.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 
 # Contact: lh3
-# Version: 0.1.0
+# Version: 0.1.2 (03JAN2009)
 
 use strict;
 use warnings;
@@ -83,10 +83,10 @@ sub export2sam_aux {
   # coor
   my $has_coor = 0;
   $s->[2] = "*";
-  if ($t[10] eq 'NM') {
-	$s->[1] |= 0x8; # unmapped
+  if ($t[10] eq 'NM' || $t[10] eq 'QC') {
+	$s->[1] |= 0x4; # unmapped
   } elsif ($t[10] =~ /(\d+):(\d+):(\d+)/) {
-	$s->[1] |= 0x8; # TODO: should I set BAM_FUNMAP in this case?
+	$s->[1] |= 0x4; # TODO: should I set BAM_FUNMAP in this case?
 	push(@$s, "H0:i:$1", "H1:i:$2", "H2:i:$3")
   } else {
 	$s->[2] = $t[10];