From 2b70735e256a35e7f697d96dc80e1f40bcf50ae4 Mon Sep 17 00:00:00 2001
From: "Brian P. Walenz" <thebri@gmail.com>
Date: Mon, 28 Jun 2021 14:08:58 -0400
Subject: [PATCH] Fix _rare_ crash when placing reads in abnormally short tigs.

---
 src/bogart/AS_BAT_PlaceReadUsingOverlaps.C | 2 +-
 src/bogart/AS_BAT_Unitig.C                 | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
index d29f703c3..1ed53783e 100644
--- a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
+++ b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
@@ -124,7 +124,7 @@ placeRead_fromOverlaps(TigVector          &tigs,
     if (ovl[oo].b_hang > 0)
       bposlen -= ovl[oo].b_hang;
 
-    if (bposlen < 0) {
+    if (bposlen <= 0) {
       writeLog("WARNING: read %u overlap to read %u in tig %u at %d-%d - hangs %d %d to large for placement, ignoring overlap\n",
                ovl[oo].a_iid,
                ovl[oo].b_iid,
diff --git a/src/bogart/AS_BAT_Unitig.C b/src/bogart/AS_BAT_Unitig.C
index 1f22c0b7a..fe4401667 100644
--- a/src/bogart/AS_BAT_Unitig.C
+++ b/src/bogart/AS_BAT_Unitig.C
@@ -390,9 +390,10 @@ Unitig::overlapConsistentWithTig(double deviations,
   int32  nBelow = 0;
   int32  nAbove = 0;
 
-  assert(bgn <  end);
-  assert(bgn <  getLength());
-  assert(end <= getLength());
+  if ((bgn >= end) ||           //  If the read placement is garbage,
+      (bgn >= getLength()) ||   //  the placement is not consistent!
+      (end >  getLength()))     //  (used to just assert on these,
+    return(1.0);                //   and they almost never occur)
 
   //  If this is a singleton tig - we should only be here when finding graph edges to repeats -
   //  we've got nothing to go on, so default to 'consistent'.