void GffRecord::printNull(QuickString &outBuf) const
{
outBuf.append(".\t.\t.\t-1\t-1\t.\t.\t.", 17);
if (_numFields > 8) {
outBuf.append("\t.", 2);
}
}
void VcfRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const {
outBuf.append(_chrName);
outBuf.append('\t');
outBuf.append(_startPosStr);
printOtherFields(outBuf);
}
void Bed3Interval::print(QuickString &outBuf) const
{
outBuf.append(_chrName);
outBuf.append('\t');
outBuf.append(_startPos);
outBuf.append('\t');
outBuf.append(_endPos);
}
void Bed3Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
{
outBuf.append(_chrName);
outBuf.append('\t');
outBuf.append(start);
outBuf.append('\t');
outBuf.append(end);
}
void BedPlusInterval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
{
Bed6Interval::print(outBuf, start, end);
for (int i=0; i < (int)_otherIdxs.size(); i++) {
outBuf.append('\t');
outBuf.append(*(_otherIdxs[i]));
}
}
void ContextBase::setErrorMsg(QuickString &msg, bool onlyWarn, const Record * record, QuickString str1, const QuickString str2, const QuickString str3) {
if (onlyWarn) {
msg = "\n***** WARNING: ";
} else {
msg = "\n***** ERROR: ";
}
msg.append(str1);
msg.append(str2);
msg.append(str3);
msg.append(" Exiting...\n");
if (record != NULL) {
record->print(msg);
}
}
void VcfRecord::printOtherFields(QuickString &outBuf) const {
outBuf.append('\t');
outBuf.append(_name);
outBuf.append('\t');
outBuf.append(_varAlt);
outBuf.append('\t');
outBuf.append(_varRef);
outBuf.append('\t');
outBuf.append(_score);
for (int i= 0; i < (int)_otherIdxs.size(); i++) {
outBuf.append('\t');
outBuf.append(*(_otherIdxs[i]));
}
}
void GffRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
{
outBuf.append(_chrName);
outBuf.append('\t');
outBuf.append(_source);
outBuf.append('\t');
outBuf.append(_name);
outBuf.append('\t');
outBuf.append(start);
outBuf.append('\t');
outBuf.append(end);
outBuf.append('\t');
printRemainingFields(outBuf);
}
void GffRecord::print(QuickString &outBuf) const
{
outBuf.append(_chrName);
outBuf.append('\t');
outBuf.append(_source);
outBuf.append('\t');
outBuf.append(_name);
outBuf.append('\t');
outBuf.append(_startPosStr);
outBuf.append('\t');
outBuf.append(_endPosStr);
outBuf.append('\t');
printRemainingFields(outBuf);
}
void VcfRecord::printOtherFields(QuickString &outBuf) const {
outBuf.append('\t');
outBuf.append(_name);
outBuf.append('\t');
outBuf.append(_varRef);
outBuf.append('\t');
outBuf.append(_varAlt);
outBuf.append('\t');
outBuf.append(_score);
outBuf.append('\t');
_plusFields.printFields(outBuf);
}
bool BufferedStreamMgr::getLine(QuickString &line)
{
line.clear();
if (_mainBufCurrStartPos >= _mainBufCurrLen) {
if (!readFileChunk()) {
_eof = true;
return false;
}
}
while (1) {
int searchPos = _mainBufCurrStartPos;
while (searchPos < _mainBufCurrLen && _mainBuf[searchPos] != '\n') {
searchPos++;
}
line.append((char *)_mainBuf + _mainBufCurrStartPos, searchPos - _mainBufCurrStartPos);
_mainBufCurrStartPos = searchPos +1;
if (searchPos == _mainBufCurrLen) { //hit end of buffer, but no newline yet
if (!readFileChunk()) { //hit eof
return true;
}
} else if (_mainBuf[searchPos] == '\n') {
return true;
}
}
}
void BedPlusInterval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
{
Bed3Interval::print(outBuf, start, end);
outBuf.append('\t');
printBed6PlusFields(outBuf);
_plusFields.printFields(outBuf);
}
OneStringBase& QuickString<quickSize>::substr(int pos, int sublen)
{
// Check sublen flag. If -1, then go to the end of the QuickString
if(sublen == -1)
{
// Calculate the size from the position to the end of the QuickString
sublen = size() - pos;
}
// Check for valid index
if((pos >= quickSize) || (pos < 0))
{
ioc << cat_error << ta_bold << fg_red << "QuickString Error:" <<
" Index Out of Bounds" << io_end;
return *this;
}
// If the substring size is too large throw an error
else if(sublen + pos > size())
{
ioc << cat_error << ta_bold << fg_red << "QuickString Error: " <<
"Size exceeds limits of QuickString"<<io_end;
return *this;
}
else
{
// Create a new OneString and append each character that is found
// in the substring
QuickString<quickSize>* newPaw = new QuickString();
for(int i = 0; i < sublen; i++)
{
newPaw->append(master[pos]);
pos++;
}
return *newPaw;
}
}
void BedPlusInterval::printNull(QuickString &outBuf) const
{
Bed6Interval::printNull(outBuf);
for (int i=startOtherIdx; i < _numPrintFields; i++) {
outBuf.append("\t.");
}
}
void ComplementFile::printRecord(int endPos)
{
_outRecord.setStartPos(_currStartPos);
QuickString startStr;
startStr.append(_currStartPos);
_outRecord.setStartPosStr(startStr);
_outRecord.setEndPos(endPos);
QuickString endStr;
endStr.append(endPos);
_outRecord.setEndPosStr(endStr);
_outputMgr->printRecord(&_outRecord);
_outputMgr->newline();
}
void GffPlusRecord::printNull(QuickString &outBuf) const
{
GffRecord::printNull(outBuf);
for (int i=_numFields; i < _numPrintFields; i++) {
outBuf.append("\t.");
}
}
void BedPlusInterval::printNull(QuickString &outBuf) const
{
Bed3Interval::printNull(outBuf);
printBed6PlusNullFields(outBuf);
for (int i=_numFixedFields; i < _numPrintFields; i++) {
outBuf.append("\t.");
}
}
void GroupBy::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
{
const Record *rec = hits.getKey();
const QuickString &opVal = _context->getColumnOpsVal(hits);
if (upCast(_context)->printFullCols()) {
outputMgr->printRecord(rec, opVal);
} else {
QuickString outBuf;
for (int i=0; i < (int)_groupCols.size(); i++) {
outBuf.append(rec->getField(_groupCols[i]));
outBuf.append('\t');
}
outBuf.append(opVal);
outputMgr->printRecord(NULL, outBuf);
}
}
Record *BlockMgr::allocateAndAssignRecord(const Record *keyRecord, int startPos, int endPos)
{
Record *record = _blockRecordsMgr->allocateRecord();
record->setChrName(keyRecord->getChrName());
record->setChromId(keyRecord->getChromId());
record->setStartPos(startPos);
record->setEndPos(endPos);
QuickString startPosStr;
QuickString endPosStr;
startPosStr.append(startPos);
endPosStr.append(endPos);
record->setStartPosStr(startPosStr);
record->setEndPosStr(endPosStr);
record->setName(keyRecord->getName());
record->setScore(keyRecord->getScore());
record->setStrand(keyRecord->getStrand());
return record;
}
void BamRecord::printUnmapped(QuickString &outBuf) const {
outBuf.append(_chrName.empty() ? "." : _chrName);
outBuf.append("\t-1\t-1\t");
outBuf.append(_name.empty() ? "." : _name);
outBuf.append('\t');
outBuf.append(_score.empty() ? "." : _score);
outBuf.append("\t.\t-1\t-1\t-1\t0,0,0\t0\t.\t."); // dot for strand, -1 for blockStarts and blockEnd
}
void GffRecord::printRemainingFields(QuickString &outBuf) const
{
outBuf.append(_score);
outBuf.append('\t');
outBuf.append(_strand);
outBuf.append('\t');
outBuf.append(_frame);
if (_numFields == 9) {
outBuf.append('\t');
outBuf.append(_group);
}
}
void BedPlusInterval::printBed6PlusFields(QuickString &outBuf) const {
if (_numFixedFields != defaultNumFixedFields) {
outBuf.append(_name);
outBuf.append('\t');
outBuf.append(_score);
outBuf.append('\t');
outBuf.append(_strand);
outBuf.append('\t');
}
}
bool BufferedStreamMgr::getLine(QuickString &line)
{
line.clear();
if (_mainBufCurrStartPos >= _mainBufCurrLen) {
if (!readFileChunk()) {
_eof = true;
return false;
}
}
bool retVal = true;
while (1) {
int searchPos = _mainBufCurrStartPos;
while (searchPos < _mainBufCurrLen && _mainBuf[searchPos] != '\n') {
searchPos++;
}
line.append((char *)_mainBuf + _mainBufCurrStartPos, searchPos - _mainBufCurrStartPos);
_mainBufCurrStartPos = searchPos +1;
if (searchPos == _mainBufCurrLen) { //hit end of buffer, but no newline yet
if (!readFileChunk()) { //hit eof
retVal = true;
break;
}
} else if (_mainBuf[searchPos] == '\n') {
retVal = true;
break;
}
}
//strip any whitespace characters, such as DOS newline characters or extra tabs,
//from the end of the line
int lastPos = line.size();
while (isspace(line[lastPos-1])) lastPos--;
line.resize(lastPos);
return retVal;
}
void BedGraphInterval::print(QuickString &outBuf) const
{
Bed3Interval::print(outBuf);
outBuf.append('\t');
outBuf.append(_name);
}
void BedGraphInterval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
{
Bed3Interval::print(outBuf, start, end);
outBuf.append('\t');
outBuf.append(_name);
}
void SingleLineDelimTextFileReader::appendField(int fieldNum, QuickString &str) const {
int startPos = _delimPositions[fieldNum] +1;
int endPos = _delimPositions[fieldNum+1];
str.append(_sLine.c_str() + startPos, endPos - startPos);
}
void BedGraphInterval::printNull(QuickString &outBuf) const
{
Bed3Interval::printNull(outBuf);
outBuf.append("\t.", 2);
}
void Bed3Interval::printNull(QuickString &outBuf) const {
outBuf.append(".\t-1\t-1", 7);
}
void VcfRecord::printNull(QuickString &outBuf) const {
outBuf.append(".\t-1\t.\t.\t.\t-1");
for (int i= startOtherIdx; i < _numPrintFields; i++) {
outBuf.append("\t.");
}
}
void BedPlusInterval::printBed6PlusNullFields(QuickString &outBuf) const {
if (_numFixedFields != defaultNumFixedFields) {
outBuf.append("\t.\t.\t.");
}
}