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#include "HDFAlnInfoGroup.hpp"
using namespace std;
int HDFAlnInfoGroup::InitializeNumPasses() {
numPasses.Initialize(alnInfoGroup, "NumPasses");
return 1;
}
void HDFAlnInfoGroup::InitializeDefaultColumnNames(vector<string> &defaultColumnNames) {
defaultColumnNames.push_back("AlnID");
defaultColumnNames.push_back("AlnGroupID");
defaultColumnNames.push_back("MovieID");
defaultColumnNames.push_back("RefGroupID");
defaultColumnNames.push_back("tStart");
defaultColumnNames.push_back("tEnd");
defaultColumnNames.push_back("RCRefStrand");
defaultColumnNames.push_back("HoleNumber");
defaultColumnNames.push_back("SetNumber");
defaultColumnNames.push_back("StrobeNumber");
defaultColumnNames.push_back("MoleculeID");
defaultColumnNames.push_back("rStart");
defaultColumnNames.push_back("rEnd");
defaultColumnNames.push_back("MapQV");
defaultColumnNames.push_back("nM");
defaultColumnNames.push_back("nMM");
defaultColumnNames.push_back("nIns");
defaultColumnNames.push_back("nDel");
defaultColumnNames.push_back("Offset_begin");
defaultColumnNames.push_back("Offset_end");
defaultColumnNames.push_back("nBackRead");
defaultColumnNames.push_back("nReadOverlap");
}
bool HDFAlnInfoGroup::Create(HDFGroup &parent) {
parent.AddGroup("AlnInfo");
// Make sure it was created, and intialize this group to reference the newly created one.
if (alnInfoGroup.Initialize(parent.group, "AlnInfo") == 0) { return 0; }
vector<string> defaultColumnNames;
InitializeDefaultColumnNames(defaultColumnNames);
columnNames.Create(alnInfoGroup.group, "ColumnNames", defaultColumnNames);
alnIndexArray.Create(&alnInfoGroup.group, "AlnIndex", defaultColumnNames.size());
return true;
}
int HDFAlnInfoGroup::Initialize(HDFGroup &rootGroup) {
if (alnInfoGroup.Initialize(rootGroup.group, "AlnInfo") == 0) { return 0; }
if (alnIndexArray.Initialize(alnInfoGroup, "AlnIndex") == 0) { return 0; }
/*
* This functionality should go into the python.
if (!alnIndexArray.ContainsAttribute("ColumnNames")) {
try {
vector<string> defaultColumnNames;
InitializeDefaultColumnNames(defaultColumnNames);
columnNames.Create(alnIndexArray.dataset, "ColumnNames", defaultColumnNames);
}
catch(Execption e) {
//
// If the dataset is not writable
}
}
*/
return 1;
}
HDFAlnInfoGroup::~HDFAlnInfoGroup() {
alnInfoGroup.Close();
}
// Return size of /AlnInfo/AlnIndex in KB
UInt HDFAlnInfoGroup::GetAlnIndexSize() {
return alnIndexArray.GetNRows() / 1024 * sizeof (unsigned int) * NCols;
}
void HDFAlnInfoGroup::Read(AlnInfo &alnInfo) {
UInt nAlignments = alnIndexArray.GetNRows();
alnInfo.alignments.resize(nAlignments);
UInt alignmentIndex;
UInt alignmentRow[NCols];
for (alignmentIndex = 0; alignmentIndex < nAlignments; alignmentIndex++) {
// Input the values.
alnIndexArray.Read(alignmentIndex, alignmentIndex + 1, alignmentRow);
alnInfo.alignments[alignmentIndex].StoreAlignmentIndex(alignmentRow, NCols);
}
}
int HDFAlnInfoGroup::GetNAlignments() {
return alnIndexArray.GetNRows();
}
unsigned int HDFAlnInfoGroup::WriteAlnIndex(vector<unsigned int> &aln) {
alnIndexArray.WriteRow(&aln[0], aln.size());
return alnIndexArray.GetNRows();
}
void HDFAlnInfoGroup::ReadCmpAlignment(UInt alignmentIndex, CmpAlignment &cmpAlignment) {
UInt alignmentRow[NCols];
alnIndexArray.Read(alignmentIndex, alignmentIndex + 1, alignmentRow);
cmpAlignment.StoreAlignmentIndex(alignmentRow, NCols);
}
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