X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phase.c;fp=phase.c;h=dfe3eeac3a5282511bc5e3c965734a03989e979c;hb=62132098eef06eaaa854bd6f39a5bae5ca5e019f;hp=aa88921c3c6a45f85231a5011e3cccd3bae2d433;hpb=213027e3cf754de8f601d3155899119f952fe617;p=samtools.git

diff --git a/phase.c b/phase.c
index aa88921..dfe3eea 100644
--- a/phase.c
+++ b/phase.c
@@ -177,7 +177,7 @@ static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
 			f->phase = c[0] > c[1]? 0 : 1;
 			f->in = c[f->phase]; f->out = c[1 - f->phase];
 			f->phased = f->in == f->out? 0 : 1;
-			f->ambig = (f->in && f->out && f->in <= f->out + 1)? 1 : 0;
+			f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
 			// fix chimera
 			f->flip = 0;
 			if (flip && c[0] >= 3 && c[1] >= 3) {