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/*
* Copyright (C) 2011-2012 Regents of the University of Michigan,
* Hyun Min Kang, Matthew Flickenger, Matthew Snyder,
* and Goncalo Abecasis
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "VcfRecordInfo.h"
#include <string>
VcfRecordInfo::VcfRecordInfo()
{
reset();
}
VcfRecordInfo::~VcfRecordInfo()
{
}
bool VcfRecordInfo::read(IFILE filePtr)
{
// Clear out any previously set values.
reset();
if(ifeof(filePtr))
{
// End of file, just return false.
return(false);
}
static const std::string keyStopChars = "\n\t;=";
static const std::string valueStopChars = "\n\t;";
// The start of the first character in stopChars
// that means there is more information for this object, so
// continue reading the file.
static const int contPos = 2;
static const int tabPos = 1;
// Keep reading. Loop will be exited
// when a \t, \n, or EOF is found.
int stopPos = contPos;
while(stopPos >= contPos)
{
// Get the next element to write the key into.
InfoElement& nextElement = myInfo.getNextEmpty();
// Read the next key.
stopPos = filePtr->readTilChar(keyStopChars, nextElement.key);
if(keyStopChars[stopPos] == '=')
{
// Stoped at the value part, so read the value
// associated with the key.
stopPos = filePtr->readTilChar(valueStopChars, nextElement.value);
}
}
// Return whether or not a tab was found at the end of the field.
return(stopPos == tabPos);
}
bool VcfRecordInfo::write(IFILE filePtr)
{
// If there are no entries, write '.'.
int infoSize = myInfo.size();
if(infoSize <= 0)
{
return(ifprintf(filePtr, "%c", EMPTY_INFO) == 1);
}
int numWritten = 0;
int numExpected = 0;
for(int i = 0; i < infoSize; i++)
{
if(i != 0)
{
numWritten += ifprintf(filePtr, ";");
++numExpected;
}
InfoElement& info = myInfo.get(i);
if(info.value.empty())
{
// No value, just a key.
numWritten += ifprintf(filePtr, "%s", info.key.c_str());
numExpected += info.key.size();
}
else
{
// write the key & the value.
numWritten += ifprintf(filePtr, "%s=%s", info.key.c_str(),
info.value.c_str());
numExpected += info.key.size() + info.value.size() + 1;
}
}
return(numWritten == numExpected);
}
void VcfRecordInfo::reset()
{
myInfo.reset();
}
void VcfRecordInfo::setString(const char* key, const char* stringVal)
{
// Check if the field is already there.
int infoSize = myInfo.size();
for(int i = 0; i < infoSize; i++)
{
InfoElement& info = myInfo.get(i);
if(info.key.compare(key) == 0)
{
// Set the value and return.
info.value = stringVal;
return;
}
}
// Not found, so add a new entry.
InfoElement& newElement = myInfo.getNextEmpty();
newElement.key = key;
newElement.value = stringVal;
}
const std::string* VcfRecordInfo::getString(const char* key)
{
// Check if the field is already there.
int infoSize = myInfo.size();
for(int i = 0; i < infoSize; i++)
{
InfoElement& info = myInfo.get(i);
if(info.key.compare(key) == 0)
{
// Found, so return the value.
return(&(info.value));
}
}
// Not found, so return NULL..
return(NULL);
}
const std::string* VcfRecordInfo::getString(int index)
{
if(index >= myInfo.size())
{
// Out of range.
return(NULL);
}
return(&(myInfo.get(index).value));
}
std::pair<std::string, std::string> VcfRecordInfo::getInfoPair(int index) const
{
if (index < myInfo.size())
{
InfoElement& e = myInfo.get(index);
return std::pair<std::string, std::string>(e.key, e.value);
}
return std::pair<std::string, std::string>();
}
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