1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
|
// Author: Yuan Li
#include <hdf/HDFRegionsWriter.hpp>
HDFRegionsWriter::HDFRegionsWriter(const std::string &filename, HDFGroup &parentGroup,
const std::vector<std::string> ®ionTypes)
: HDFWriterBase(filename), parentGroup_(parentGroup), regionTypes_(regionTypes), curRow_(0)
{
// Initialize the 'regions' group.
regionsArray_.Initialize(parentGroup_, PacBio::GroupNames::regions, RegionAnnotation::NCOLS);
}
HDFRegionsWriter::~HDFRegionsWriter(void)
{
WriteAttributes();
Close();
}
bool HDFRegionsWriter::WriteAttributes(void)
{
if (curRow_ > 0) {
/*
AddAttribute<std::vector<std::string>>(regionsArray_,
PacBio::AttributeNames::Regions::columnnames,
PacBio::AttributeValues::Regions::columnnames);
AddAttribute<std::vector<std::string>>(
regionsArray_, PacBio::AttributeNames::Regions::regiontypes, regionTypes_);
AddAttribute<std::vector<std::string>>(
regionsArray_, PacBio::AttributeNames::Regions::regiondescriptions,
PacBio::AttributeValues::Regions::regiondescriptions);
AddAttribute<std::vector<std::string>>(regionsArray_,
PacBio::AttributeNames::Regions::regionsources,
PacBio::AttributeValues::Regions::regionsources);
*/
return true;
} else {
AddErrorMessage("Could not write attributes when Regions group is empty.");
return false;
}
}
bool HDFRegionsWriter::Write(const std::vector<RegionAnnotation> &annotations)
{
for (auto annotation : annotations)
if (not Write(annotation)) return false;
return true;
}
bool HDFRegionsWriter::Write(const RegionAnnotation &annotation)
{
try {
regionsArray_.WriteRow(annotation.row, HDFRegionsWriter::NCOLS);
} catch (H5::Exception &e) {
std::ostringstream sout;
sout << "Failed to write region annotation " << annotation.GetHoleNumber();
AddErrorMessage(sout.str());
return false;
}
++curRow_;
return true;
}
void HDFRegionsWriter::Flush(void) { regionsArray_.Flush(); }
void HDFRegionsWriter::Close(void)
{
Flush();
regionsArray_.Close();
}
|
