From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 12 Mar 2013 13:25:17 +0000 (+0000)
Subject: Merge remote branch 'remotes/master/master' into fb-annots
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=60e0a8467ddbd0b89f15d201dcfe10c8796552b2

Merge remote branch 'remotes/master/master' into fb-annots
---

60e0a8467ddbd0b89f15d201dcfe10c8796552b2
diff --cc bcftools/call1.c
index eb58498,bc1cd40..18805a0
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@@ -544,10 -522,10 +552,10 @@@ int bcfview(int argc, char *argv[]
  			int i;
  			for (i = 0; i < 9; ++i) em[i] = -1.;
  		}
-         if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+         if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
          {
              bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
 -            int gts = call_multiallelic_gt(b,p1,vc.min_ma_lrt);
 +            int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
              if ( gts<=1 && vc.flag & VC_VARONLY ) continue;
          }
  		else if (vc.flag & VC_CALL) { // call variants