minor changes to a heuristic rule

[samtools.git] / phase.c

diff --git a/phase.c b/phase.c
index aa88921c3c6a45f85231a5011e3cccd3bae2d433..dfe3eeac3a5282511bc5e3c965734a03989e979c 100644 (file)
--- 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) {