C++ BamAlignment::RemoveTag方法代码示例

// reverts a BAM alignment
// default behavior (for now) is : replace Qualities with OQ, clear IsDuplicate flag
// can override default behavior using command line options
void RevertTool::RevertToolPrivate::RevertAlignment(BamAlignment& al) {

    // replace Qualities with OQ, if requested
    if ( !m_settings->IsKeepQualities ) {
        string originalQualities;
        if ( al.GetTag(m_OQ, originalQualities) ) {
            al.Qualities = originalQualities;
            al.RemoveTag(m_OQ);
        }
    }

    // clear duplicate flag, if requested
    if ( !m_settings->IsKeepDuplicateFlag )
        al.SetIsDuplicate(false);
}

void ReadContainerTest::test_ParseRead() {
  map<pair<string,int>, string> ref_ext_nucleotides;
  BamAlignment aln;
  std::string rg = "test";
  std::string repseq = "AC";
  AlignedRead aligned_read;
  float copynum = 10;
  include_flank = false;
  // Test valid allele length
  aln.Name = "test";
  aln.QueryBases = "NNNNN";
  aln.Qualities = "NNNNN";
  aln.SetIsReverseStrand(true);
  aln.Position = 0;
  aln.SetIsSecondMate(false);
  aln.AddTag("RG","Z",rg);
  aln.AddTag("XS","i",0);
  aln.AddTag("XE","i",20);
  aln.AddTag("XR", "Z", repseq);
  aln.AddTag("XC", "f", copynum);
  aln.RefID = 0;
  // No XD
  aln.RemoveTag("XD");
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides))); 
  // Test more valid allele lengths
  aln.AddTag("XD","i",20);
  CPPUNIT_ASSERT(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides));
  aln.RemoveTag("XD");
  aln.AddTag("XD","i",-19);
  CPPUNIT_ASSERT(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides));
  // Test invalid allele length
  aln.RemoveTag("XD");
  aln.AddTag("XD","i",-31);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  // Exceed max_diff_ref
  aln.RemoveTag("XD");
  aln.AddTag("XD","i",100);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  aln.RemoveTag("XD");
  aln.AddTag("XD","i",0);
  // Exceed max mate dist
  aln.AddTag("XM","i",1000000);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  aln.RemoveTag("XM");
  // Exceed max mapq
  aln.AddTag("XQ","i",10000);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  aln.RemoveTag("XQ");
  // Read is mate
  aln.SetIsSecondMate(true);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  aln.SetIsSecondMate(false);
  // Read is partial
  aln.AddTag("XP","i",1);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  aln.RemoveTag("XP");
  // Non-unit
  unit = true;
  aln.RemoveTag("XD");
  aln.AddTag("XD","i",5);
  CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
  unit = false;
}

void ReadContainerTest::test_GetBamTags() {
  // TODO
  BamAlignment aln;
  string str_result;
  float float_result;
  string rg = "test";
  float xc = 12.0;
  aln.AddTag("RG","Z",rg);
  aln.AddTag("XD","i",0);
  aln.AddTag("XC","f",xc);
  // GetStringBamTag
  CPPUNIT_ASSERT(_read_container->GetStringBamTag(aln, "RG", &str_result));
  CPPUNIT_ASSERT(str_result == "test");
  CPPUNIT_ASSERT(!_read_container->GetStringBamTag(aln, "XX", &str_result));
  // GetFloatBamTag
  CPPUNIT_ASSERT(_read_container->GetFloatBamTag(aln, "XC", &float_result));
  CPPUNIT_ASSERT(float_result == 12.0);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XX", &float_result));
  // GetIntBamTag
  int int_result;
  int d = 0;
  aln.AddTag("XA","i",d);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 0);
  aln.RemoveTag("XA");
  int8_t d8 = 10;
  aln.AddTag("XA","c", d8);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 10);
  aln.RemoveTag("XA");
  aln.AddTag("XA","c",rg);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XA", &float_result));
  aln.RemoveTag("XA");
  uint8_t ud8 = 9;
  aln.AddTag("XA","C", ud8);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 9);
  aln.RemoveTag("XA");
  aln.AddTag("XA","C",rg);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XA", &float_result));
  aln.RemoveTag("XA");
  int16_t d16 = 8;
  aln.AddTag("XA","s",d16);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 8);
  aln.RemoveTag("XA");
  aln.AddTag("XA","s",rg);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XA", &float_result));
  aln.RemoveTag("XA");
  uint16_t ud16 = 7;
  aln.AddTag("XA","S",ud16);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 7);
  aln.RemoveTag("XA");
  aln.AddTag("XA","S",rg);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XA", &float_result));
  aln.RemoveTag("XA");
  uint32_t ud32 = 6;
  aln.AddTag("XA","I",ud32);
  CPPUNIT_ASSERT(_read_container->GetIntBamTag(aln, "XA", &int_result));
  CPPUNIT_ASSERT_EQUAL(int_result, 6);
  aln.RemoveTag("XA");
  aln.AddTag("XA","I",rg);
  CPPUNIT_ASSERT(!_read_container->GetFloatBamTag(aln, "XA", &float_result));
  aln.RemoveTag("XA");
}

void setMateInfo( BamAlignment & rec1, BamAlignment & rec2, SamHeader & header) {
    const int NO_ALIGNMENT_REFERENCE_INDEX = -1;
    const int NO_ALIGNMENT_START = -1;
    // If neither read is unmapped just set their mate info
    if (rec1.IsMapped() && rec2.IsMapped()) {
        
        rec1.MateRefID = rec2.MateRefID;
        rec1.MatePosition = rec2.Position;
        rec1.SetIsReverseStrand(rec2.IsReverseStrand());
        rec1.SetIsMapped(true);
        rec1.AddTag("MQ", "i", rec2.MapQuality);
        
        rec2.MateRefID = rec1.RefID;
        rec2.MatePosition = rec1.Position;
        rec2.SetIsReverseStrand( rec1.IsReverseStrand() );
        rec2.SetIsMapped(true);
        rec2.AddTag("MQ", "i", rec1.MapQuality);
    }
    // Else if they're both unmapped set that straight
    else if (!rec1.IsMapped() && !rec2.IsMapped()) {
        rec1.RefID = NO_ALIGNMENT_REFERENCE_INDEX;
        rec1.Position = NO_ALIGNMENT_START;
        rec1.MateRefID = NO_ALIGNMENT_REFERENCE_INDEX;
        rec1.MatePosition = NO_ALIGNMENT_START;
        rec1.SetIsReverseStrand(rec2.IsReverseStrand());
        rec1.SetIsMapped(false);
        rec2.RemoveTag("MQ");
        rec1.Length = 0;
        
        rec2.RefID = NO_ALIGNMENT_REFERENCE_INDEX;
        rec2.Position = NO_ALIGNMENT_START;
        rec2.MateRefID = NO_ALIGNMENT_REFERENCE_INDEX;
        rec2.MatePosition = NO_ALIGNMENT_START;
        rec2.SetIsReverseStrand(rec1.IsReverseStrand());
        rec2.SetIsMapped(false);
        rec2.RemoveTag("MQ");
        rec2.Length = 0;
    }
    // And if only one is mapped copy it's coordinate information to the mate
    else {
        BamAlignment & mapped   = rec1.IsMapped() ? rec1 : rec2;
        BamAlignment & unmapped = rec1.IsMapped() ? rec2 : rec1;
        unmapped.RefID = mapped.RefID;
        unmapped.Position = mapped.Position;
        
        mapped.MateRefID = unmapped.RefID;
        mapped.MatePosition = unmapped.Position;
        mapped.SetIsMateReverseStrand(unmapped.IsReverseStrand());
        mapped.SetIsMateMapped(false);
        mapped.Length = 0;
        
        unmapped.MateRefID = mapped.RefID;
        unmapped.MatePosition = mapped.Position;
        unmapped.SetIsMateReverseStrand(mapped.IsReverseStrand());
        unmapped.SetIsMateMapped(true);
        unmapped.Length = 0;
    }
    
    const int insertSize = computeInsertSize(rec1, rec2);
    rec1.Length = insertSize;
    rec2.Length = -insertSize;
}