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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 "BamInterface.h"
#include "CharBuffer.h"
BamInterface::BamInterface()
{
}
BamInterface::~BamInterface()
{
}
// Read a BAM file's header.
bool BamInterface::readHeader(IFILE filePtr, SamFileHeader& header,
SamStatus& status)
{
if(filePtr == NULL)
{
// File is not open, return false.
status.setStatus(SamStatus::FAIL_ORDER,
"Cannot read header since the file pointer is null");
return(false);
}
if(filePtr->isOpen() == false)
{
status.setStatus(SamStatus::FAIL_ORDER,
"Cannot read header since the file is not open");
return(false);
}
// Clear the passed in header.
header.resetHeader();
int32_t headerLength;
int readSize = ifread(filePtr, &headerLength, sizeof(headerLength));
if(readSize != sizeof(headerLength))
{
String errMsg = "Failed to read the BAM header length, read ";
errMsg += readSize;
errMsg += " bytes instead of ";
errMsg += (unsigned int)sizeof(headerLength);
status.setStatus(SamStatus::FAIL_IO, errMsg.c_str());
return(false);
}
String headerStr;
if(headerLength > 0)
{
// Read the header.
readSize =
ifread(filePtr, headerStr.LockBuffer(headerLength + 1), headerLength);
headerStr[headerLength] = 0;
headerStr.UnlockBuffer();
if(readSize != headerLength)
{
// Failed to read the header.
status.setStatus(SamStatus::FAIL_IO, "Failed to read the BAM header.");
return(false);
}
}
// Parse the header that was read.
if(!header.addHeader(headerStr))
{
// Status is set in the method on failure.
status.setStatus(SamStatus::FAIL_PARSE, header.getErrorMessage());
return(false);
}
int referenceCount;
// Read the number of references sequences.
ifread(filePtr, &referenceCount, sizeof(int));
// Get and clear the reference info so it can be set
// from the bam reference table.
SamReferenceInfo& refInfo =
header.getReferenceInfoForBamInterface();
refInfo.clear();
CharBuffer refName;
// Read each reference sequence
for (int i = 0; i < referenceCount; i++)
{
int nameLength;
int rc;
// Read the length of the reference name.
rc = ifread(filePtr, &nameLength, sizeof(int));
if(rc != sizeof(int))
{
status.setStatus(SamStatus::FAIL_IO,
"Failed to read the BAM reference dictionary.");
return(false);
}
// Read the name.
refName.readFromFile(filePtr, nameLength);
// Read the length of the reference sequence.
int32_t refLen;
rc = ifread(filePtr, &refLen, sizeof(int));
if(rc != sizeof(int)) {
status.setStatus(SamStatus::FAIL_IO,
"Failed to read the BAM reference dictionary.");
return(false);
}
refInfo.add(refName.c_str(), refLen);
}
// Successfully read the file.
return(true);
}
bool BamInterface::writeHeader(IFILE filePtr, SamFileHeader& header,
SamStatus& status)
{
if((filePtr == NULL) || (filePtr->isOpen() == false))
{
// File is not open, return false.
status.setStatus(SamStatus::FAIL_ORDER,
"Cannot write header since the file pointer is null");
return(false);
}
char magic[4];
magic[0] = 'B';
magic[1] = 'A';
magic[2] = 'M';
magic[3] = 1;
// Write magic to the file.
ifwrite(filePtr, magic, 4);
////////////////////////////////
// Write the header to the file.
////////////////////////////////
// Construct a string containing the entire header.
std::string headerString = "";
header.getHeaderString(headerString);
int32_t headerLen = headerString.length();
int numWrite = 0;
// Write the header length.
numWrite = ifwrite(filePtr, &headerLen, sizeof(int32_t));
if(numWrite != sizeof(int32_t))
{
status.setStatus(SamStatus::FAIL_IO,
"Failed to write the BAM header length.");
return(false);
}
// Write the header to the file.
numWrite = ifwrite(filePtr, headerString.c_str(), headerLen);
if(numWrite != headerLen)
{
status.setStatus(SamStatus::FAIL_IO,
"Failed to write the BAM header.");
return(false);
}
////////////////////////////////////////////////////////
// Write the Reference Information.
const SamReferenceInfo& refInfo = header.getReferenceInfo();
// Get the number of sequences.
int32_t numSeq = refInfo.getNumEntries();
ifwrite(filePtr, &numSeq, sizeof(int32_t));
// Write each reference sequence
for (int i = 0; i < numSeq; i++)
{
const char* refName = refInfo.getReferenceName(i);
// Add one for the null value.
int32_t nameLength = strlen(refName) + 1;
// Write the length of the reference name.
ifwrite(filePtr, &nameLength, sizeof(int32_t));
// Write the name.
ifwrite(filePtr, refName, nameLength);
// Write the length of the reference sequence.
int32_t refLen = refInfo.getReferenceLength(i);
ifwrite(filePtr, &refLen, sizeof(int32_t));
}
return(true);
}
void BamInterface::readRecord(IFILE filePtr, SamFileHeader& header,
SamRecord& record,
SamStatus& samStatus)
{
// TODO - need to validate there are @SQ lines in both sam/bam - MAYBE!
// SetBufferFromFile will reset the record prior to reading a new one.
if(record.setBufferFromFile(filePtr, header) != SamStatus::SUCCESS)
{
// Failed, so add the error message.
samStatus.addError(record.getStatus());
}
}
SamStatus::Status BamInterface::writeRecord(IFILE filePtr,
SamFileHeader& header,
SamRecord& record,
SamRecord::SequenceTranslation translation)
{
// Write the file, returning the status.
return(record.writeRecordBuffer(filePtr, translation));
}
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