From 10cbc7dfb5f0bd87690f8b2be83db9e763739df0 Mon Sep 17 00:00:00 2001 From: Claire Lemaitre Date: Tue, 1 Mar 2022 17:27:53 +0100 Subject: [PATCH] making the bed option compatible with the branching filter --- src/FindBreakpoints.hpp | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/src/FindBreakpoints.hpp b/src/FindBreakpoints.hpp index a2889e4..c875720 100644 --- a/src/FindBreakpoints.hpp +++ b/src/FindBreakpoints.hpp @@ -503,18 +503,28 @@ void FindBreakpoints::operator()() end_pos=get<1>(interval_vector.front()); } - if(!(*m_it_kmer).isValid() || (m_positionm_solid_stretch_size = 0; this->m_gap_stretch_size = 0; this->m_kmer_begin = KmerCanonical(); this->m_kmer_end = KmerCanonical(); - //DEBUG - //cout<<"n"; + } - + + if(m_position==start_pos-1) //for each beginning of bed region + { + //Re-initialize stretch_size for each bed region + this->m_solid_stretch_size = 0; + this->m_gap_stretch_size = 0; + this->m_kmer_begin = KmerCanonical(); + this->m_kmer_end = KmerCanonical(); + + //Re-initialize het_kmer_history for each bed region + memset(this->m_het_kmer_history, 0, sizeof(info_type)*256); + } + if(((*m_it_kmer).isValid()) && (m_position>=start_pos)) //inside the current bed interval {