Commit 2e291b19 authored by mourisl's avatar mourisl Committed by Li Song
Browse files

Fix a serious issue of comparing SAM mapping record that causes paired-end dedup errors

parent 06aacab5

src/chromap.h

+1 −1
Original line number Diff line number Diff line
@@ -34,7 +34,7 @@ 
#include "temp_mapping.h"

#include "utils.h"



#define CHROMAP_VERSION "0.3.0-r509"

#define CHROMAP_VERSION "0.3.1-r510"



namespace chromap {

src/sam_mapping.h

+6 −5
Original line number Diff line number Diff line
@@ -201,13 +201,14 @@ class SAMMapping : public Mapping { 
  bool operator<(const SAMMapping &m) const {

    int read1_flag = flag_ & BAM_FREAD1;

    int m_read1_flag = m.flag_ & BAM_FREAD1;

    return std::tie(rid_, pos_, cell_barcode_, mapq_, mrid_, mpos_, read_id_, read1_flag) <

           std::tie(m.rid_, m.pos_, m.cell_barcode_, m.mapq_, m.mrid_, m.mpos_, m.read_id_,

                    m_read1_flag);

    return std::tie(rid_, pos_, cell_barcode_, mrid_, mpos_, read1_flag, mapq_, read_id_) <

           std::tie(m.rid_, m.pos_, m.cell_barcode_, m.mrid_, m.mpos_, m_read1_flag, m.mapq_, m.read_id_);

  }

  bool operator==(const SAMMapping &m) const {

    return std::tie(pos_, rid_, cell_barcode_, is_rev_, mrid_, mpos_) ==

           std::tie(m.pos_, m.rid_, m.cell_barcode_, m.is_rev_, m.mrid_, m.mpos_);

    int read1_flag = flag_ & BAM_FREAD1;

    int m_read1_flag = m.flag_ & BAM_FREAD1;

    return std::tie(pos_, rid_, cell_barcode_, read1_flag, mrid_, mpos_) ==

           std::tie(m.pos_, m.rid_, m.cell_barcode_, m_read1_flag, m.mrid_, m.mpos_);

  }

  bool IsSamePosition(const SAMMapping &m) const {

    return std::tie(pos_, rid_, is_rev_, mrid_, mpos_) ==

CRA Git | Maintained and supported by SUSTech CRA and CCSE