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

diff --cc bam_plcmd.c
Simple merge

diff --cc bcftools/call1.c
index eb584987d4c4a23b1c8fcab33332e701536dd149,bc1cd407e7967290051b4ffbf4c73938468a43dd..18805a03e7b76ab8db3040cc6e9d87a5e16dadaa
--- 1/bcftools/call1.c
--- 2/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

diff --cc bcftools/prob1.c
Simple merge

diff --cc samtools.1
Simple merge