diff --git a/src/bogart/AS_BAT_Instrumentation.C b/src/bogart/AS_BAT_Instrumentation.C index 8c5257328..d8498e514 100644 --- a/src/bogart/AS_BAT_Instrumentation.C +++ b/src/bogart/AS_BAT_Instrumentation.C @@ -272,11 +272,20 @@ classifyTigsAsUnassembled(TigVector &tigs, bool r4 = classifyRule4(utg, F, nCoverage, bCoverage, lowcovFraction, lowcovDepth); // If either first or last read is flagged as a bubble, it's not unassembled. + // + // Sept 2020 - bri isn't sure if this is being clever about something or + // not. When bubbles are assigned - search for setBubble - we're both + // setting the tig _isBubble to true and labelling all reads as + // isBubble(). Could we then be merging a bubble into something else? + // The asserts were added. if ((OG->isBubble(utg->firstRead()->ident) == true) || (OG->isBubble(utg-> lastRead()->ident) == true)) bb = true; + if (bb == true) assert(utg->_isBubble == true); + if (bb == false) assert(utg->_isBubble == false); + // If flagged, we're done, just move on. if ((bb == false) && (rr == false) && (rs || r1 || r2 || r3 || r4))