TEST(BamHeaderTest, ExtractFromRawDataOk)
{
ReadGroupInfo rg1("rg1");
rg1.Sample("control");
ReadGroupInfo rg2("rg2");
rg2.Sample("condition1");
ReadGroupInfo rg3("rg3");
rg3.Sample("condition1");
SequenceInfo seq1("chr1");
seq1.Length("2038").Species("chocobo");
SequenceInfo seq2("chr2");
seq2.Length("3042").Species("chocobo");
ProgramInfo prog1("_foo_");
prog1.Name("ide");
BamHeader header;
header.Version("1.1")
.SortOrder("queryname")
.PacBioBamVersion("3.0.1")
.AddReadGroup(rg1)
.AddReadGroup(rg2)
.AddReadGroup(rg3)
.AddSequence(seq1)
.AddSequence(seq2)
.AddProgram(prog1)
.AddComment("ipsum and so on")
.AddComment("citation needed");
const string& expectedText = "@HD\tVN:1.1\tSO:queryname\tpb:3.0.1\n"
"@SQ\tSN:chr1\tLN:2038\tSP:chocobo\n"
"@SQ\tSN:chr2\tLN:3042\tSP:chocobo\n"
"@RG\tID:rg1\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:control\tPM:SEQUEL\n"
"@RG\tID:rg2\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@RG\tID:rg3\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@PG\tID:_foo_\tPN:ide\n"
"@CO\tipsum and so on\n"
"@CO\tcitation needed\n";
string text = header.ToSam();
PBBAM_SHARED_PTR<bam_hdr_t> rawData(sam_hdr_parse(text.size(), text.c_str()), tests::BamHdrDeleter());
rawData->ignore_sam_err = 0;
rawData->cigar_tab = NULL;
rawData->l_text = text.size();
rawData->text = (char*)calloc(rawData->l_text + 1, 1);
memcpy(rawData->text, text.c_str(), rawData->l_text);
const BamHeader newHeader = BamHeader(string(rawData->text, rawData->l_text));
EXPECT_EQ(header.Version(), newHeader.Version());
EXPECT_EQ(header.SortOrder(), newHeader.SortOrder());
EXPECT_EQ(header.PacBioBamVersion(), newHeader.PacBioBamVersion());
text = newHeader.ToSam();
EXPECT_EQ(expectedText, text);
}
PBBAM_SHARED_PTR<bam_hdr_t> BamHeaderMemory::MakeRawHeader(const BamHeader& header)
{
const string& text = header.ToSam();
PBBAM_SHARED_PTR<bam_hdr_t> rawData(sam_hdr_parse(text.size(), text.c_str()), internal::HtslibHeaderDeleter());
rawData->ignore_sam_err = 0;
rawData->cigar_tab = NULL;
rawData->l_text = text.size();
rawData->text = (char*)calloc(rawData->l_text + 1, 1);
memcpy(rawData->text, text.c_str(), rawData->l_text);
return rawData;
}
TEST(BamHeaderTest, MergeHandlesDuplicateReadGroups)
{
const string hdrText = {
"@HD\tVN:1.1\tSO:unknown\tpb:3.0.1\n"
"@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;"
"InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;"
"SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\t"
"PU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0\tPM:SEQUEL\n"
"@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0\n"
"@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2\n"
};
// duplicate @RG:IDs handled ok (i.e. not duplicated in output)
const BamHeader header1(hdrText);
const BamHeader header2(hdrText);
const BamHeader merged = header1 + header2;
EXPECT_EQ(hdrText, merged.ToSam());
}
TEST(BamHeaderTest, EncodeTest)
{
ReadGroupInfo rg1("rg1");
rg1.Sample("control");
ReadGroupInfo rg2("rg2");
rg2.Sample("condition1");
ReadGroupInfo rg3("rg3");
rg3.Sample("condition1");
SequenceInfo seq1("chr1");
seq1.Length("2038").Species("chocobo");
SequenceInfo seq2("chr2");
seq2.Length("3042").Species("chocobo");
ProgramInfo prog1("_foo_");
prog1.Name("ide");
BamHeader header;
header.Version("1.1")
.SortOrder("queryname")
.PacBioBamVersion("3.0.1")
.AddReadGroup(rg1)
.AddReadGroup(rg2)
.AddReadGroup(rg3)
.AddSequence(seq1)
.AddSequence(seq2)
.AddProgram(prog1)
.AddComment("ipsum and so on")
.AddComment("citation needed");
const string& expectedText = "@HD\tVN:1.1\tSO:queryname\tpb:3.0.1\n"
"@SQ\tSN:chr1\tLN:2038\tSP:chocobo\n"
"@SQ\tSN:chr2\tLN:3042\tSP:chocobo\n"
"@RG\tID:rg1\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:control\tPM:SEQUEL\n"
"@RG\tID:rg2\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@RG\tID:rg3\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@PG\tID:_foo_\tPN:ide\n"
"@CO\tipsum and so on\n"
"@CO\tcitation needed\n";
const string& text = header.ToSam();
EXPECT_EQ(expectedText, text);
}
TEST(BamHeaderTest, MergeOk)
{
const string hdrText1 = {
"@HD\tVN:1.1\tSO:unknown\tpb:3.0.1\n"
"@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;"
"InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;"
"SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\t"
"PU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0\t"
"PM:SEQUEL\n"
"@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0\n"
"@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2\n"
"@CO\tcomment1\n"
};
const string hdrText2 = {
"@HD\tVN:1.1\tSO:unknown\tpb:3.0.1\n"
"@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;"
"InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;"
"PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;"
"PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;"
"BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;"
"FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\t"
"PM:SEQUEL\n"
"@PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0\n"
"@PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0\n"
"@PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0\n"
"@CO\tcomment2\n"
};
const string mergedText = {
"@HD\tVN:1.1\tSO:unknown\tpb:3.0.1\n"
"@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;"
"InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;"
"SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\t"
"PU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0\t"
"PM:SEQUEL\n"
"@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;"
"InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;"
"PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;"
"PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;"
"BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;"
"FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\t"
"PM:SEQUEL\n"
"@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0\n"
"@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2\n"
"@PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0\n"
"@PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0\n"
"@PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0\n"
"@CO\tcomment1\n"
"@CO\tcomment2\n"
};
{ // operator+
const BamHeader header1(hdrText1);
const BamHeader header2(hdrText2);
const BamHeader merged = header1 + header2;
EXPECT_EQ(mergedText, merged.ToSam());
// also make sure inputs not changed
EXPECT_EQ(hdrText1, header1.ToSam());
EXPECT_EQ(hdrText2, header2.ToSam());
}
{ // operator+=
BamHeader header1(hdrText1);
header1 += BamHeader(hdrText2);
EXPECT_EQ(mergedText, header1.ToSam());
}
}
