void testReadBam()
{
SamFile inSam;
assert(inSam.OpenForRead("testFiles/testBam.bam"));
// Call generic test which since the sam and bam are identical, should
// contain the same results.
testRead(inSam);
inSam.Close();
testFlagRead("testFiles/testBam.bam");
}
bool BamProcessor::finalize (bool success)
{
if (outfile_.IsOpen ())
{
trclog << "Closing output file" << std::endl;
outfile_.Close ();
}
if (logfile_.is_open ())
{
time_t t = time (NULL);
print_stats (logfile_);
logfile_ << "\nFinished " << (success ? "successfully" : "due to error") << " at " << asctime (localtime (&t)) << "\n";
trclog << "Closing log file" << std::endl;
logfile_.close ();
}
if (info.enabled ())
print_stats (info.o_);
return true;
}
int Dedup_LowMem::execute(int argc, char** argv)
{
/* --------------------------------
* process the arguments
* -------------------------------*/
String inFile, outFile, logFile;
myDoRecab = false;
bool removeFlag = false;
bool verboseFlag = false;
myForceFlag = false;
myNumMissingMate = 0;
myMinQual = DEFAULT_MIN_QUAL;
String excludeFlags = "0xB04";
uint16_t intExcludeFlags = 0;
bool noeof = false;
bool params = false;
LongParamContainer parameters;
parameters.addGroup("Required Parameters");
parameters.addString("in", &inFile);
parameters.addString("out", &outFile);
parameters.addGroup("Optional Parameters");
parameters.addInt("minQual", & myMinQual);
parameters.addString("log", &logFile);
parameters.addBool("oneChrom", &myOneChrom);
parameters.addBool("recab", &myDoRecab);
parameters.addBool("rmDups", &removeFlag);
parameters.addBool("force", &myForceFlag);
parameters.addString("excludeFlags", &excludeFlags);
parameters.addBool("verbose", &verboseFlag);
parameters.addBool("noeof", &noeof);
parameters.addBool("params", ¶ms);
parameters.addPhoneHome(VERSION);
myRecab.addRecabSpecificParameters(parameters);
ParameterList inputParameters;
inputParameters.Add(new LongParameters ("Input Parameters",
parameters.getLongParameterList()));
// parameters start at index 2 rather than 1.
inputParameters.Read(argc, argv, 2);
// If no eof block is required for a bgzf file, set the bgzf file type to
// not look for it.
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
if(inFile.IsEmpty())
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "Specify an input file" << std::endl;
return EXIT_FAILURE;
}
if(outFile.IsEmpty())
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "Specify an output file" << std::endl;
return EXIT_FAILURE;
}
intExcludeFlags = excludeFlags.AsInteger();
if(myForceFlag && SamFlag::isDuplicate(intExcludeFlags))
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "Cannot specify --force and Duplicate in the excludeFlags. Since --force indicates to override"
<< " previous duplicate setting and the excludeFlags says to skip those, you can't do both.\n";
return EXIT_FAILURE;
}
if(!SamFlag::isSecondary(intExcludeFlags))
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "ERROR: Secondary reads must be excluded, edit --excludeFlags to include 0x0100\n";
return EXIT_FAILURE;
}
if(!(intExcludeFlags & SamFlag::SUPPLEMENTARY_ALIGNMENT))
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "ERROR: Supplementary reads must be excluded, edit --excludeFlags to include 0x0800\n";
return EXIT_FAILURE;
}
if(logFile.IsEmpty())
{
logFile = outFile + ".log";
}
if(myDoRecab)
{
int status = myRecab.processRecabParam();
if(status != 0)
{
inputParameters.Status();
return(status);
}
}
if(params)
{
inputParameters.Status();
}
Logger::gLogger = new Logger(logFile.c_str(), verboseFlag);
/* -------------------------------------------------------------------
* The arguments are processed. Prepare the input BAM file,
* instantiate dedup_LowMem, and construct the read group library map
* ------------------------------------------------------------------*/
SamFile samIn;
samIn.OpenForRead(inFile.c_str());
// If the file isn't sorted it will throw an exception.
samIn.setSortedValidation(SamFile::COORDINATE);
SamFileHeader header;
samIn.ReadHeader(header);
buildReadGroupLibraryMap(header);
lastReference = -1;
lastCoordinate = -1;
// for keeping some basic statistics
uint32_t recordCount = 0;
uint32_t pairedCount = 0;
uint32_t properPairCount = 0;
uint32_t unmappedCount = 0;
uint32_t reverseCount = 0;
uint32_t qualCheckFailCount = 0;
uint32_t secondaryCount = 0;
uint32_t supplementaryCount = 0;
uint32_t excludedCount = 0;
// Now we start reading records
SamRecord* recordPtr;
SamStatus::Status returnStatus = SamStatus::SUCCESS;
while(returnStatus == SamStatus::SUCCESS)
{
recordPtr = mySamPool.getRecord();
if(recordPtr == NULL)
{
std::cerr << "Failed to allocate enough records\n";
return(-1);
}
if(!samIn.ReadRecord(header, *recordPtr))
{
returnStatus = samIn.GetStatus();
continue;
}
// Take note of properties of this record
int flag = recordPtr->getFlag();
if(SamFlag::isPaired(flag)) ++pairedCount;
if(SamFlag::isProperPair(flag)) ++properPairCount;
if(SamFlag::isReverse(flag)) ++reverseCount;
if(SamFlag::isQCFailure(flag)) ++qualCheckFailCount;
if(SamFlag::isSecondary(flag)) ++secondaryCount;
if(flag & SamFlag::SUPPLEMENTARY_ALIGNMENT) ++supplementaryCount;
if(!SamFlag::isMapped(flag)) ++unmappedCount;
// put the record in the appropriate maps:
// single reads go in myFragmentMap
// paired reads go in myPairedMap
recordCount = samIn.GetCurrentRecordCount();
// if we have moved to a new position, look back at previous reads for duplicates
if (hasPositionChanged(*recordPtr))
{
cleanupPriorReads(recordPtr);
}
// Determine if this read should be checked for duplicates.
if((!SamFlag::isMapped(flag)) || ((flag & intExcludeFlags) != 0))
{
++excludedCount;
// No deduping done on this record, but still build the recab table.
if(myDoRecab)
{
myRecab.processReadBuildTable(*recordPtr);
}
// Nothing more to do with this record, so
// release the pointer.
mySamPool.releaseRecord(recordPtr);
}
else
{
if(SamFlag::isDuplicate(flag) && !myForceFlag)
{
// Error: Marked duplicates, and duplicates aren't excluded.
Logger::gLogger->error("There are records already duplicate marked.");
Logger::gLogger->error("Use -f to clear the duplicate flag and start the dedup_LowMem procedure over");
}
checkDups(*recordPtr, recordCount);
mySamPool.releaseRecord(recordPtr);
}
// let the user know we're not napping
if (verboseFlag && (recordCount % 100000 == 0))
{
Logger::gLogger->writeLog("recordCount=%u singleKeyMap=%u pairedKeyMap=%u, dictSize=%u",
recordCount, myFragmentMap.size(),
myPairedMap.size(),
myMateMap.size());
}
}
// we're finished reading record so clean up the duplicate search and
// close the input file
cleanupPriorReads(NULL);
samIn.Close();
// print some statistics
Logger::gLogger->writeLog("--------------------------------------------------------------------------");
Logger::gLogger->writeLog("SUMMARY STATISTICS OF THE READS");
Logger::gLogger->writeLog("Total number of reads: %u",recordCount);
Logger::gLogger->writeLog("Total number of paired-end reads: %u",
pairedCount);
Logger::gLogger->writeLog("Total number of properly paired reads: %u",
properPairCount);
Logger::gLogger->writeLog("Total number of unmapped reads: %u",
unmappedCount);
Logger::gLogger->writeLog("Total number of reverse strand mapped reads: %u",
reverseCount);
Logger::gLogger->writeLog("Total number of QC-failed reads: %u",
qualCheckFailCount);
Logger::gLogger->writeLog("Total number of secondary reads: %u",
secondaryCount);
Logger::gLogger->writeLog("Total number of supplementary reads: %u",
supplementaryCount);
Logger::gLogger->writeLog("Size of singleKeyMap (must be zero): %u",
myFragmentMap.size());
Logger::gLogger->writeLog("Size of pairedKeyMap (must be zero): %u",
myPairedMap.size());
Logger::gLogger->writeLog("Total number of missing mates: %u",
myNumMissingMate);
Logger::gLogger->writeLog("Total number of reads excluded from duplicate checking: %u",
excludedCount);
Logger::gLogger->writeLog("--------------------------------------------------------------------------");
Logger::gLogger->writeLog("Sorting the indices of %d duplicated records",
myDupList.size());
// sort the indices of duplicate records
std::sort(myDupList.begin(), myDupList.end(),
std::less<uint32_t> ());
// get ready to write the output file by making a second pass
// through the input file
samIn.OpenForRead(inFile.c_str());
samIn.ReadHeader(header);
SamFile samOut;
samOut.OpenForWrite(outFile.c_str());
samOut.WriteHeader(header);
// If we are recalibrating, output the model information.
if(myDoRecab)
{
myRecab.modelFitPrediction(outFile);
}
// an iterator to run through the duplicate indices
int currentDupIndex = 0;
bool moreDups = !myDupList.empty();
// let the user know what we're doing
Logger::gLogger->writeLog("\nWriting %s", outFile.c_str());
// count the duplicate records as a check
uint32_t singleDuplicates(0), pairedDuplicates(0);
// start reading records and writing them out
SamRecord record;
while(samIn.ReadRecord(header, record))
{
uint32_t currentIndex = samIn.GetCurrentRecordCount();
bool foundDup = moreDups &&
(currentIndex == myDupList[currentDupIndex]);
// modify the duplicate flag and write out the record,
// if it's appropriate
int flag = record.getFlag();
if (foundDup)
{
// this record is a duplicate, so mark it.
record.setFlag( flag | 0x400 );
currentDupIndex++;
// increment duplicate counters to verify we found them all
if ( ( ( flag & 0x0001 ) == 0 ) || ( flag & 0x0008 ) )
{ // unpaired or mate unmapped
singleDuplicates++;
}
else
{
pairedDuplicates++;
}
// recalibrate if necessary.
if(myDoRecab)
{
myRecab.processReadApplyTable(record);
}
// write the record if we are not removing duplicates
if (!removeFlag ) samOut.WriteRecord(header, record);
}
else
{
if(myForceFlag)
{
// this is not a duplicate we've identified but we want to
// remove any duplicate marking
record.setFlag( flag & 0xfffffbff ); // unmark duplicate
}
// Not a duplicate, so recalibrate if necessary.
if(myDoRecab)
{
myRecab.processReadApplyTable(record);
}
samOut.WriteRecord(header, record);
}
// Let the user know we're still here
if (verboseFlag && (currentIndex % 100000 == 0)) {
Logger::gLogger->writeLog("recordCount=%u", currentIndex);
}
}
// We're done. Close the files and print triumphant messages.
samIn.Close();
samOut.Close();
Logger::gLogger->writeLog("Successfully %s %u unpaired and %u paired duplicate reads",
removeFlag ? "removed" : "marked" ,
singleDuplicates,
pairedDuplicates/2);
Logger::gLogger->writeLog("\nDedup_LowMem complete!");
return 0;
}
int Bam2FastQ::execute(int argc, char **argv)
{
// Extract command line arguments.
String inFile = "";
bool readName = false;
String refFile = "";
String firstOut = "";
String secondOut = "";
String unpairedOut = "";
bool interleave = false;
bool noeof = false;
bool gzip = false;
bool params = false;
myOutBase = "";
myNumMateFailures = 0;
myNumPairs = 0;
myNumUnpaired = 0;
mySplitRG = false;
myQField = "";
myNumQualTagErrors = 0;
myReverseComp = true;
myRNPlus = false;
myFirstRNExt = DEFAULT_FIRST_EXT;
mySecondRNExt = DEFAULT_SECOND_EXT;
myCompression = InputFile::DEFAULT;
ParameterList inputParameters;
BEGIN_LONG_PARAMETERS(longParameterList)
LONG_PARAMETER_GROUP("Required Parameters")
LONG_STRINGPARAMETER("in", &inFile)
LONG_PARAMETER_GROUP("Optional Parameters")
LONG_PARAMETER("readName", &readName)
LONG_PARAMETER("splitRG", &mySplitRG)
LONG_STRINGPARAMETER("qualField", &myQField)
LONG_PARAMETER("merge", &interleave)
LONG_STRINGPARAMETER("refFile", &refFile)
LONG_STRINGPARAMETER("firstRNExt", &myFirstRNExt)
LONG_STRINGPARAMETER("secondRNExt", &mySecondRNExt)
LONG_PARAMETER("rnPlus", &myRNPlus)
LONG_PARAMETER("noReverseComp", &myReverseComp)
LONG_PARAMETER("gzip", &gzip)
LONG_PARAMETER("noeof", &noeof)
LONG_PARAMETER("params", ¶ms)
LONG_PARAMETER_GROUP("Optional OutputFile Names")
LONG_STRINGPARAMETER("outBase", &myOutBase)
LONG_STRINGPARAMETER("firstOut", &firstOut)
LONG_STRINGPARAMETER("secondOut", &secondOut)
LONG_STRINGPARAMETER("unpairedOut", &unpairedOut)
LONG_PHONEHOME(VERSION)
END_LONG_PARAMETERS();
inputParameters.Add(new LongParameters ("Input Parameters",
longParameterList));
// parameters start at index 2 rather than 1.
inputParameters.Read(argc, argv, 2);
// If no eof block is required for a bgzf file, set the bgzf file type to
// not look for it.
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
if(gzip)
{
myCompression = InputFile::GZIP;
}
// Check to see if the in file was specified, if not, report an error.
if(inFile == "")
{
usage();
inputParameters.Status();
// In file was not specified but it is mandatory.
std::cerr << "--in is a mandatory argument, "
<< "but was not specified" << std::endl;
return(-1);
}
// Cannot specify both interleaved & secondOut since secondOut would be N/A.
if(interleave && !secondOut.IsEmpty())
{
usage();
inputParameters.Status();
std::cerr << "ERROR: Cannot specify --merge & --secondOut.\n";
return(-1);
}
// Cannot specify both interleaved & secondOut since secondOut would be N/A.
if(interleave && !secondOut.IsEmpty())
{
usage();
inputParameters.Status();
std::cerr << "ERROR: Cannot specify --merge & --secondOut.\n";
return(-1);
}
// Cannot specify both splitRG & firstOut/secondOut/unpairedOut
// since it needs a different file for each RG.
if(mySplitRG && (!firstOut.IsEmpty() ||
!secondOut.IsEmpty() || !unpairedOut.IsEmpty()))
{
usage();
inputParameters.Status();
std::cerr << "ERROR: Cannot specify --splitRG & --firstOut/--secondOut/--unpairedOut.\n";
std::cerr << "Use --outBase instead.\n";
return(-1);
}
// Cannot specify splitRG & output to stdout.
if(mySplitRG && (myOutBase[0] == '-'))
{
usage();
inputParameters.Status();
std::cerr << "ERROR: Cannot specify --splitRG & write to stdout.\n";
return(-1);
}
// Check to see if the out file was specified, if not, generate it from
// the input filename.
if(myOutBase == "")
{
// Just remove the extension from the input filename.
int extStart = inFile.FastFindLastChar('.');
if(extStart <= 0)
{
myOutBase = inFile;
}
else
{
myOutBase = inFile.Left(extStart);
}
}
if(mySplitRG)
{
std::string fqList = myOutBase.c_str();
fqList += ".list";
myFqList = ifopen(fqList.c_str(), "w");
ifprintf(myFqList, "MERGE_NAME\tFASTQ1\tFASTQ2\tRG\n");
}
// Check to see if the first/second/single-ended were specified and
// if not, set them.
myFirstFileNameExt = "_1.fastq";
mySecondFileNameExt = "_2.fastq";
myUnpairedFileNameExt = ".fastq";
if(interleave)
{
myFirstFileNameExt = "_interleaved.fastq";
myFirstFileNameExt = "_interleaved.fastq";
}
getFileName(firstOut, myFirstFileNameExt);
getFileName(secondOut, mySecondFileNameExt);
getFileName(unpairedOut, myUnpairedFileNameExt);
if(params)
{
inputParameters.Status();
}
// Open the files for reading/writing.
// Open prior to opening the output files,
// so if there is an error, the outputs don't get created.
SamFile samIn;
samIn.OpenForRead(inFile, &mySamHeader);
// Skip non-primary reads.
samIn.SetReadFlags(0, 0x0100);
// Open the output files if not splitting RG
if(!mySplitRG)
{
myUnpairedFile = ifopen(unpairedOut, "w", myCompression);
// Only open the first file if it is different than an already opened file.
if(firstOut != unpairedOut)
{
myFirstFile = ifopen(firstOut, "w", myCompression);
}
else
{
myFirstFile = myUnpairedFile;
}
// If it is interleaved or the 2nd file is not a new name, set it appropriately.
if(interleave || secondOut == firstOut)
{
mySecondFile = myFirstFile;
}
else if(secondOut == unpairedOut)
{
mySecondFile = myUnpairedFile;
}
else
{
mySecondFile = ifopen(secondOut, "w", myCompression);
}
if(myUnpairedFile == NULL)
{
std::cerr << "Failed to open " << unpairedOut
<< " so can't convert bam2FastQ.\n";
return(-1);
}
if(myFirstFile == NULL)
{
std::cerr << "Failed to open " << firstOut
<< " so can't convert bam2FastQ.\n";
return(-1);
}
if(mySecondFile == NULL)
{
std::cerr << "Failed to open " << secondOut
<< " so can't convert bam2FastQ.\n";
return(-1);
}
}
if((readName) || (strcmp(mySamHeader.getSortOrder(), "queryname") == 0))
{
readName = true;
}
else
{
// defaulting to coordinate sorted.
samIn.setSortedValidation(SamFile::COORDINATE);
}
// Setup the '=' translation if the reference was specified.
if(!refFile.IsEmpty())
{
GenomeSequence* refPtr = new GenomeSequence(refFile);
samIn.SetReadSequenceTranslation(SamRecord::BASES);
samIn.SetReference(refPtr);
}
SamRecord* recordPtr;
int16_t samFlag;
SamStatus::Status returnStatus = SamStatus::SUCCESS;
while(returnStatus == SamStatus::SUCCESS)
{
recordPtr = myPool.getRecord();
if(recordPtr == NULL)
{
// Failed to allocate a new record.
throw(std::runtime_error("Failed to allocate a new SAM/BAM record"));
}
if(!samIn.ReadRecord(mySamHeader, *recordPtr))
{
// Failed to read a record.
returnStatus = samIn.GetStatus();
continue;
}
// Have a record. Check to see if it is a pair or unpaired read.
samFlag = recordPtr->getFlag();
if(SamFlag::isPaired(samFlag))
{
if(readName)
{
handlePairedRN(*recordPtr);
}
else
{
handlePairedCoord(*recordPtr);
}
}
else
{
++myNumUnpaired;
writeFastQ(*recordPtr, myUnpairedFile,
myUnpairedFileNameExt);
}
}
// Flush All
cleanUpMateMap(0, true);
if(returnStatus == SamStatus::NO_MORE_RECS)
{
returnStatus = SamStatus::SUCCESS;
}
samIn.Close();
closeFiles();
// Output the results
std::cerr << "\nFound " << myNumPairs << " read pairs.\n";
std::cerr << "Found " << myNumUnpaired << " unpaired reads.\n";
if(myNumMateFailures != 0)
{
std::cerr << "Failed to find mates for " << myNumMateFailures
<< " reads, so they were written as unpaired\n"
<< " (not included in either of the above counts).\n";
}
if(myNumQualTagErrors != 0)
{
std::cerr << myNumQualTagErrors << " records did not have tag "
<< myQField.c_str() << " or it was invalid, so the quality field was used for those records.\n";
}
return(returnStatus);
}
int main(int argc, char ** argv)
{
gpLogger = new Logger;
static struct option getopt_long_options[] =
{
// Input options
{ "fasta", required_argument, NULL, 'f'},
{ "in", required_argument, NULL, 'i'},
{ "out", required_argument, NULL, 'o'},
{ "verbose", no_argument, NULL, 'v'},
{ "log", required_argument, NULL, 'l'},
{ "clear", no_argument, NULL, 0},
{ "AS", required_argument, NULL, 0},
{ "UR", required_argument, NULL, 0},
{ "SP", required_argument, NULL, 0},
{ "HD", required_argument, NULL, 0},
{ "RG", required_argument, NULL, 0},
{ "PG", required_argument, NULL, 0},
{ "checkSQ", no_argument, NULL, 0},
{ NULL, 0, NULL, 0 },
};
int n_option_index = 0, c;
std::string sAS, sUR, sSP, sFasta, sInFile, sOutFile, sLogFile;
bool bClear, bCheckSQ, bVerbose;
std::vector<std::string> vsHDHeaders, vsRGHeaders, vsPGHeaders;
bCheckSQ = bVerbose = false;
bClear = true;
while ( (c = getopt_long(argc, argv, "vf:i:o:l:", getopt_long_options, &n_option_index)) != -1 ) {
// std::cout << getopt_long_options[n_option_index].name << "\t" << optarg << std::endl;
if ( c == 'f' ) {
sFasta = optarg;
}
else if ( c == 'i' ) {
sInFile = optarg;
}
else if ( c == 'o' ) {
sOutFile = optarg;
}
else if ( c == 'v' ) {
bVerbose = true;
}
else if ( c == 'l' ) {
sLogFile = optarg;
}
else if ( strcmp(getopt_long_options[n_option_index].name,"AS") == 0 ) {
sAS = optarg;
}
else if ( strcmp(getopt_long_options[n_option_index].name,"UR") == 0 ) {
sUR = optarg;
}
else if ( strcmp(getopt_long_options[n_option_index].name,"SP") == 0 ) {
sSP = optarg;
}
else if ( strcmp(getopt_long_options[n_option_index].name,"HD") == 0 ) {
vsHDHeaders.push_back(optarg);
}
else if ( strcmp(getopt_long_options[n_option_index].name,"RG") == 0 ) {
vsRGHeaders.push_back(optarg);
}
else if ( strcmp(getopt_long_options[n_option_index].name,"PG") == 0 ) {
vsPGHeaders.push_back(optarg);
}
else if ( strcmp(getopt_long_options[n_option_index].name,"checkSQ") == 0 ) {
bCheckSQ = true;
}
else {
std::cerr << "Error: Unrecognized option " << getopt_long_options[n_option_index].name << std::endl;
abort();
}
}
if ( optind < argc ) {
printUsage(std::cerr);
gpLogger->error("non-option argument %s exist ",argv[optind]);
}
if ( sInFile.empty() || sOutFile.empty() ) {
printUsage(std::cerr);
gpLogger->error("Input and output files are required");
}
if ( sLogFile.compare("__NONE__") == 0 ) {
sLogFile = (sOutFile + ".log");
}
gpLogger->open(sLogFile.c_str(), bVerbose);
if ( ( bCheckSQ ) && ( sFasta.empty() ) ) {
printUsage(std::cerr);
gpLogger->error("--checkSQ option must be used with --fasta option");
}
// check whether each header line starts with a correct tag
checkHeaderStarts(vsHDHeaders, "@HD\t");
checkHeaderStarts(vsRGHeaders, "@RG\t");
checkHeaderStarts(vsPGHeaders, "@PG\t");
gpLogger->write_log("Arguments in effect:");
gpLogger->write_log("\t--in [%s]",sInFile.c_str());
gpLogger->write_log("\t--out [%s]",sOutFile.c_str());
gpLogger->write_log("\t--log [%s]",sLogFile.c_str());
gpLogger->write_log("\t--fasta [%s]",sFasta.c_str());
gpLogger->write_log("\t--AS [%s]",sAS.c_str());
gpLogger->write_log("\t--UR [%s]",sUR.c_str());
gpLogger->write_log("\t--SP [%s]",sSP.c_str());
gpLogger->write_log("\t--checkSQ [%s]",bClear ? "ON" : "OFF" );
if ( vsHDHeaders.empty() ) {
gpLogger->write_log("\t--HD []");
}
else {
gpLogger->write_log("\t--HD [%s]",vsHDHeaders[0].c_str());
}
if ( vsRGHeaders.empty() ) {
gpLogger->write_log("\t--RG []");
}
else {
gpLogger->write_log("\t--RG [%s]",vsRGHeaders[0].c_str());
}
if ( vsPGHeaders.empty() ) {
gpLogger->write_log("\t--PG []");
}
else {
for(uint32_t i=0; i < vsPGHeaders.size(); ++i) {
gpLogger->write_log("\t--PG [%s]",vsPGHeaders[i].c_str());
}
}
if ( (vsHDHeaders.empty() ) && ( vsRGHeaders.empty() ) && ( vsPGHeaders.empty() ) && ( !bClear ) && ( sFasta.empty() ) ) {
gpLogger->warning("No option is in effect for modifying BAM files. The input and output files will be identical");
}
if ( ( vsHDHeaders.size() > 1 ) || ( vsRGHeaders.size() > 1 ) ) {
gpLogger->error("HD and RG headers cannot be multiple");
}
FastaFile fastaFile;
if ( ! sFasta.empty() ) {
if ( fastaFile.open(sFasta.c_str()) ) {
gpLogger->write_log("Reading the reference file %s",sFasta.c_str());
fastaFile.readThru();
fastaFile.close();
gpLogger->write_log("Finished reading the reference file %s",sFasta.c_str());
}
else {
gpLogger->error("Failed to open reference file %s",sFasta.c_str());
}
}
SamFile samIn;
SamFile samOut;
if ( ! samIn.OpenForRead(sInFile.c_str()) ) {
gpLogger->error("Cannot open BAM file %s for reading - %s",sInFile.c_str(), SamStatus::getStatusString(samIn.GetStatus()) );
}
if ( ! samOut.OpenForWrite(sOutFile.c_str()) ) {
gpLogger->error("Cannot open BAM file %s for writing - %s",sOutFile.c_str(), SamStatus::getStatusString(samOut.GetStatus()) );
}
SamFileHeader samHeader;
SamHeaderRecord* pSamHeaderRecord;
samIn.ReadHeader(samHeader);
// check the sanity of SQ file
// make sure the SN and LN matches, with the same order
if ( bCheckSQ ) {
unsigned int numSQ = 0;
while( (pSamHeaderRecord = samHeader.getNextHeaderRecord()) != NULL ) {
if ( pSamHeaderRecord->getType() == SamHeaderRecord::SQ ) {
++numSQ;
}
}
if ( numSQ != fastaFile.vsSequenceNames.size() ) {
gpLogger->error("# of @SQ tags are different from the original BAM and the reference file");
}
// iterator over all @SQ objects
for(unsigned int i=0; i < numSQ; ++i) {
pSamHeaderRecord = samHeader.getSQ(fastaFile.vsSequenceNames[i].c_str());
if ( fastaFile.vsSequenceNames[i].compare(pSamHeaderRecord->getTagValue("SN")) != 0 ) {
gpLogger->error("SequenceName is not identical between fasta and input BAM file");
}
else if ( static_cast<int>(fastaFile.vnSequenceLengths[i]) != atoi(pSamHeaderRecord->getTagValue("LN")) ) {
gpLogger->error("SequenceLength is not identical between fasta and input BAM file");
}
else {
if ( !sAS.empty() )
samHeader.setSQTag("AS",sAS.c_str(),fastaFile.vsSequenceNames[i].c_str());
samHeader.setSQTag("M5",fastaFile.vsMD5sums[i].c_str(),fastaFile.vsSequenceNames[i].c_str());
if ( !sUR.empty() )
samHeader.setSQTag("UR",sUR.c_str(),fastaFile.vsSequenceNames[i].c_str());
if ( !sSP.empty() )
samHeader.setSQTag("SP",sSP.c_str(),fastaFile.vsSequenceNames[i].c_str());
}
}
gpLogger->write_log("Finished checking the consistency of SQ tags");
}
else {
gpLogger->write_log("Skipped checking the consistency of SQ tags");
}
// go over the headers again,
// assuming order of HD, SQ, RG, PG, and put proper tags at the end of the original tags
gpLogger->write_log("Creating the header of new output file");
//SamFileHeader outHeader;
samHeader.resetHeaderRecordIter();
for(unsigned int i=0; i < vsHDHeaders.size(); ++i) {
samHeader.addHeaderLine(vsHDHeaders[i].c_str());
}
/*
for(int i=0; i < fastaFile.vsSequenceNames.size(); ++i) {
std::string s("@SQ\tSN:");
char buf[1024];
s += fastaFile.vsSequenceNames[i];
sprintf(buf,"\tLN:%d",fastaFile.vnSequenceLengths[i]);
s += buf;
if ( !sAS.empty() ) {
sprintf(buf,"\tAS:%s",sAS.c_str());
s += buf;
}
if ( !sUR.empty() ) {
sprintf(buf,"\tUR:%s",sUR.c_str());
s += buf;
}
sprintf(buf,"\tM5:%s",fastaFile.vsMD5sums[i].c_str());
s += buf;
if ( !sSP.empty() ) {
sprintf(buf,"\tSP:%s",sSP.c_str());
s += buf;
}
outHeader.addHeaderLine(s.c_str());
}*/
for(unsigned int i=0; i < vsRGHeaders.size(); ++i) {
samHeader.addHeaderLine(vsRGHeaders[i].c_str());
}
for(unsigned int i=0; i < vsPGHeaders.size(); ++i) {
samHeader.addHeaderLine(vsPGHeaders[i].c_str());
}
samOut.WriteHeader(samHeader);
gpLogger->write_log("Adding %d HD, %d RG, and %d PG headers",vsHDHeaders.size(), vsRGHeaders.size(), vsPGHeaders.size());
gpLogger->write_log("Finished writing output headers");
// parse RG tag and get RG ID to append
std::string sRGID;
if ( ! vsRGHeaders.empty() ) {
std::vector<std::string> tokens;
FastaFile::tokenizeString( vsRGHeaders[0].c_str(), tokens );
for(unsigned int i=0; i < tokens.size(); ++i) {
if ( tokens[i].find("ID:") == 0 ) {
sRGID = tokens[i].substr(3);
}
}
}
gpLogger->write_log("Writing output BAM file");
SamRecord samRecord;
while (samIn.ReadRecord(samHeader, samRecord) == true) {
if ( !sRGID.empty() ) {
if ( samRecord.addTag("RG",'Z',sRGID.c_str()) == false ) {
gpLogger->error("Failed to add a RG tag %s",sRGID.c_str());
}
// temporary code added
if ( strncmp(samRecord.getReadName(),"seqcore_",8) == 0 ) {
char buf[1024];
sprintf(buf,"UM%s",samRecord.getReadName()+8);
samRecord.setReadName(buf);
}
}
samOut.WriteRecord(samHeader, samRecord);
//if ( samIn.GetCurrentRecordCount() == 1000 ) break;
}
samOut.Close();
gpLogger->write_log("Successfully written %d records",samIn.GetCurrentRecordCount());
delete gpLogger;
return 0;
}
int ClipOverlap::execute(int argc, char **argv)
{
// Extract command line arguments.
String inFile = "";
String outFile = "";
String storeOrig = "";
bool readName = false;
bool noRNValidate = false;
bool stats = false;
int poolSize = DEFAULT_POOL_SIZE;
bool unmapped = false;
bool noeof = false;
bool params = false;
String excludeFlags = "0xF0C";
// TODO, cleanup legacy parameters
ParameterList inputParameters;
BEGIN_LONG_PARAMETERS(longParameterList)
LONG_PARAMETER_GROUP("Required Parameters")
LONG_STRINGPARAMETER("in", &inFile)
LONG_STRINGPARAMETER("out", &outFile)
LONG_PARAMETER_GROUP("Optional Parameters")
LONG_STRINGPARAMETER("storeOrig", &storeOrig)
LONG_PARAMETER("readName", &readName)
LONG_PARAMETER ("noRNValidate", &noRNValidate)
LONG_PARAMETER ("stats", &stats)
LONG_PARAMETER ("overlapsOnly", &myOverlapsOnly)
LONG_STRINGPARAMETER ("excludeFlags", &excludeFlags)
LONG_PARAMETER("unmapped", &unmapped)
LONG_PARAMETER("noeof", &noeof)
LONG_PARAMETER("params", ¶ms)
LONG_PARAMETER_GROUP("Coordinate Processing Optional Parameters")
LONG_INTPARAMETER("poolSize", &poolSize)
LONG_PARAMETER("poolSkipOverlap", &myPoolSkipOverlap)
LONG_PHONEHOME(VERSION)
BEGIN_LEGACY_PARAMETERS()
LONG_PARAMETER ("clipsOnly", &myOverlapsOnly)
LONG_PARAMETER("poolSkipClip", &myPoolSkipOverlap)
END_LONG_PARAMETERS();
inputParameters.Add(new LongParameters ("Input Parameters",
longParameterList));
// parameters start at index 2 rather than 1.
inputParameters.Read(argc, argv, 2);
// If no eof block is required for a bgzf file, set the bgzf file type to
// not look for it.
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
// Check to see if the in file was specified, if not, report an error.
if(inFile == "")
{
printUsage(std::cerr);
inputParameters.Status();
// In file was not specified but it is mandatory.
std::cerr << "--in is a mandatory argument, "
<< "but was not specified" << std::endl;
return(-1);
}
// Check to see if the out file was specified, if not, report an error.
if(outFile == "")
{
printUsage(std::cerr);
inputParameters.Status();
// Out file was not specified but it is mandatory.
std::cerr << "--out is a mandatory argument, "
<< "but was not specified" << std::endl;
return(-1);
}
if((storeOrig.Length() != 0) && (storeOrig.Length() != 2))
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "--storeOrig tag name must be 2 characters.\n";
return(-1);
}
myOverlapHandler = new OverlapClipLowerBaseQual();
if(myOverlapHandler == NULL)
{
printUsage(std::cerr);
inputParameters.Status();
std::cerr << "Failed to allocate the overlap handler\n";
return(-1);
}
if(unmapped)
{
myOverlapHandler->markAsUnmapped();
}
// Setup the overlap handler.
myOverlapHandler->keepStats(stats);
if(storeOrig.Length() != 0)
{
myOverlapHandler->storeOrigCigar(storeOrig);
}
myIntExcludeFlags = excludeFlags.AsInteger();
if(params)
{
inputParameters.Status();
}
// For each step process the file.
// Open the files & read/write the sam header.
SamStatus::Status runStatus = SamStatus::SUCCESS;
for(int i = 1; i <= myOverlapHandler->numSteps(); i++)
{
// Open the file for reading.
mySamHeader.resetHeader();
SamFile samIn(inFile, SamFile::READ, &mySamHeader);
SamFile* samOutPtr = NULL;
// Check if writing, if so, open the output file.
if(i == myOverlapHandler->numSteps())
{
samOutPtr = new SamFile(outFile, SamFile::WRITE, &mySamHeader);
}
if(readName)
{
if(!noRNValidate)
{
samIn.setSortedValidation(SamFile::QUERY_NAME);
}
runStatus = handleSortedByReadName(samIn, samOutPtr);
}
else
{
// Coordinate sorted, so work with the pools.
samIn.setSortedValidation(SamFile::COORDINATE);
myPool.setMaxAllocatedRecs(poolSize);
// Reset the number of failures
myNumMateFailures = 0;
myNumPoolFail = 0;
myNumPoolFailNoHandle = 0;
myNumPoolFailHandled = 0;
myNumOutOfOrder = 0;
// Run by coordinate
if(samOutPtr != NULL)
{
// Setup the output buffer for writing.
SamCoordOutput outputBuffer(myPool);
outputBuffer.setOutputFile(samOutPtr, &mySamHeader);
runStatus = handleSortedByCoord(samIn, &outputBuffer);
// Cleanup the output buffer.
if(!outputBuffer.flushAll())
{
std::cerr << "ERROR: Failed to flush the output buffer\n";
runStatus = SamStatus::FAIL_IO;
}
}
else
{
runStatus = handleSortedByCoord(samIn, NULL);
}
}
if(runStatus != SamStatus::SUCCESS)
{
break;
}
// Close the input file, it will be reopened if there are
// multiple steps.
samIn.Close();
if(samOutPtr != NULL)
{
samOutPtr->Close();
delete samOutPtr;
samOutPtr = NULL;
}
}
// Done processing.
// Print Stats
myOverlapHandler->printStats();
if(myNumMateFailures != 0)
{
std::cerr << "WARNING: did not find expected overlapping mates for "
<< myNumMateFailures << " records." << std::endl;
}
if(myNumPoolFail != 0)
{
// Had to skip clipping some records due to running out of
// memory and not being able to wait for the mate.
std::cerr << "WARNING: " << myNumPoolFail
<< " record pool failures\n";
if(myNumPoolFailNoHandle != 0)
{
std::cerr << "Due to hitting the max record poolSize, skipped handling "
<< myNumPoolFailNoHandle << " records." << std::endl;
}
if(myNumPoolFailHandled != 0)
{
std::cerr << "Due to hitting the max record poolSize, default handled "
<< myNumPoolFailHandled << " records." << std::endl;
}
if(myNumOutOfOrder != 0)
{
std::cerr << "WARNING: Resulting File out of Order by "
<< myNumOutOfOrder << " records.\n";
}
}
if(runStatus == SamStatus::SUCCESS)
{
if(myNumPoolFail == 0)
{
std::cerr << "Completed ClipOverlap Successfully.\n";
}
else
{
runStatus = SamStatus::NO_MORE_RECS;
std::cerr << "Completed ClipOverlap with WARNINGS.\n";
}
}
else
{
std::cerr << "Failed to complete ClipOverlap.\n";
}
return(runStatus);
}
void testFlagRead(const char* fileName)
{
SamFile inSam;
SamFileHeader samHeader;
SamRecord samRecord;
////////////////////////////////////////////////////////////
// Required flag 0x48 (only flag 73 matches)
// Exclude nothing
assert(inSam.OpenForRead(fileName));
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
inSam.SetReadFlags(0x48, 0x0);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead1(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == false);
inSam.Close();
////////////////////////////////////////////////////////////
// No required flags.
// Exclude 0x48. This leaves just the one read with flag 133.
assert(inSam.OpenForRead(fileName));
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
inSam.SetReadFlags(0x0, 0x48);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead2(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == false);
inSam.Close();
////////////////////////////////////////////////////////////
// Required flag 0x40
// Exclude 0x48.
// This will not find any records since the exclude and required conflict.
assert(inSam.OpenForRead(fileName));
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
inSam.SetReadFlags(0x40, 0x48);
assert(inSam.ReadRecord(samHeader, samRecord) == false);
inSam.Close();
////////////////////////////////////////////////////////////
// Required flag 0x4
// Exclude 0x8.
// Only finds flag 133.
assert(inSam.OpenForRead(fileName));
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
inSam.SetReadFlags(0x4, 0x8);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead2(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == false);
inSam.Close();
////////////////////////////////////////////////////////////
// Required flag 0x4
// Exclude nothing
// Finds flags 133 & 141.
assert(inSam.OpenForRead(fileName));
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
inSam.SetReadFlags(0x4, 0x0);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead2(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead8(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead10(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == false);
inSam.Close();
}
// main function
int TrimBam::execute(int argc, char ** argv)
{
SamFile samIn;
SamFile samOut;
int numTrimBaseL = 0;
int numTrimBaseR = 0;
bool noeof = false;
bool ignoreStrand = false;
bool noPhoneHome = false;
std::string inName = "";
std::string outName = "";
if ( argc < 5 ) {
usage();
std::cerr << "ERROR: Incorrect number of parameters specified\n";
return(-1);
}
inName = argv[2];
outName = argv[3];
static struct option getopt_long_options[] = {
// Input options
{ "left", required_argument, NULL, 'L'},
{ "right", required_argument, NULL, 'R'},
{ "ignoreStrand", no_argument, NULL, 'i'},
{ "noeof", no_argument, NULL, 'n'},
{ "noPhoneHome", no_argument, NULL, 'p'},
{ "nophonehome", no_argument, NULL, 'P'},
{ "phoneHomeThinning", required_argument, NULL, 't'},
{ "phonehomethinning", required_argument, NULL, 'T'},
{ NULL, 0, NULL, 0 },
};
int argIndex = 4;
if(argv[argIndex][0] != '-')
{
// This is the number of bases to trim off both sides
// so convert to a number.
numTrimBaseL = atoi(argv[argIndex]);
numTrimBaseR = numTrimBaseL;
++argIndex;
}
int c = 0;
int n_option_index = 0;
// Process any additional parameters
while ( ( c = getopt_long(argc, argv,
"L:R:in", getopt_long_options, &n_option_index) )
!= -1 )
{
switch(c)
{
case 'L':
numTrimBaseL = atoi(optarg);
break;
case 'R':
numTrimBaseR = atoi(optarg);
break;
case 'i':
ignoreStrand = true;
break;
case 'n':
noeof = true;
break;
case 'p':
case 'P':
noPhoneHome = true;
break;
case 't':
case 'T':
PhoneHome::allThinning = atoi(optarg);
break;
default:
fprintf(stderr,"ERROR: Unrecognized option %s\n",
getopt_long_options[n_option_index].name);
return(-1);
}
}
if(!noPhoneHome)
{
PhoneHome::checkVersion(getProgramName(), VERSION);
}
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
if ( ! samIn.OpenForRead(inName.c_str()) ) {
fprintf(stderr, "***Problem opening %s\n",inName.c_str());
return(-1);
}
if(!samOut.OpenForWrite(outName.c_str())) {
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}
fprintf(stderr,"Arguments in effect: \n");
fprintf(stderr,"\tInput file : %s\n",inName.c_str());
fprintf(stderr,"\tOutput file : %s\n",outName.c_str());
if(numTrimBaseL == numTrimBaseR)
{
fprintf(stderr,"\t#Bases to trim from each side : %d\n", numTrimBaseL);
}
else
{
fprintf(stderr,"\t#Bases to trim from the left of forward strands : %d\n",
numTrimBaseL);
fprintf(stderr,"\t#Bases to trim from the right of forward strands: %d\n",
numTrimBaseR);
if(!ignoreStrand)
{
// By default, reverse strands are treated the opposite.
fprintf(stderr,"\t#Bases to trim from the left of reverse strands : %d\n",
numTrimBaseR);
fprintf(stderr,"\t#Bases to trim from the right of reverse strands : %d\n",
numTrimBaseL);
}
else
{
// ignore strand, treating forward & reverse strands the same
fprintf(stderr,"\t#Bases to trim from the left of reverse strands : %d\n",
numTrimBaseL);
fprintf(stderr,"\t#Bases to trim from the right of reverse strands : %d\n",
numTrimBaseR);
}
}
// Read the sam header.
SamFileHeader samHeader;
if(!samIn.ReadHeader(samHeader))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}
// Write the sam header.
if(!samOut.WriteHeader(samHeader))
{
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}
SamRecord samRecord;
char seq[65536];
char qual[65536];
int i, len;
// Keep reading records until ReadRecord returns false.
while(samIn.ReadRecord(samHeader, samRecord)) {
// Successfully read a record from the file, so write it.
strcpy(seq,samRecord.getSequence());
strcpy(qual,samRecord.getQuality());
// Number of bases to trim from the left/right,
// set based on ignoreStrand flag and strand info.
int trimLeft = numTrimBaseL;
int trimRight = numTrimBaseR;
if(!ignoreStrand)
{
if(SamFlag::isReverse(samRecord.getFlag()))
{
// We are reversing the reverse reads,
// so swap the left & right trim counts.
trimRight = numTrimBaseL;
trimLeft = numTrimBaseR;
}
}
len = strlen(seq);
// Do not trim if sequence is '*'
if ( strcmp(seq, "*") != 0 ) {
bool qualValue = true;
if(strcmp(qual, "*") == 0)
{
qualValue = false;
}
int qualLen = strlen(qual);
if ( (qualLen != len) && qualValue ) {
fprintf(stderr,"ERROR: Sequence and Quality have different length\n");
return(-1);
}
if ( len < (trimLeft + trimRight) ) {
// Read Length is less than the total number of bases to trim,
// so trim the entire read.
for(i=0; i < len; ++i) {
seq[i] = 'N';
if ( qualValue ) {
qual[i] = '!';
}
}
}
else
{
// Read Length is larger than the total number of bases to trim,
// so trim from the left, then from the right.
for(i=0; i < trimLeft; ++i)
{
// Trim the bases from the left.
seq[i] = 'N';
if ( qualValue )
{
qual[i] = '!';
}
}
for(i = 0; i < trimRight; i++)
{
seq[len-i-1] = 'N';
if(qualValue)
{
qual[len-i-1] = '!';
}
}
}
samRecord.setSequence(seq);
samRecord.setQuality(qual);
}
if(!samOut.WriteRecord(samHeader, samRecord)) {
// Failed to write a record.
fprintf(stderr, "Failure in writing record %s\n", samOut.GetStatusMessage());
return(-1);
}
}
if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed to read a record.
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
}
std::cerr << std::endl << "Number of records read = " <<
samIn.GetCurrentRecordCount() << std::endl;
std::cerr << "Number of records written = " <<
samOut.GetCurrentRecordCount() << std::endl;
if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed reading a record.
return(samIn.GetStatus());
}
// Since the reads were successful, return the status based
samIn.Close();
samOut.Close();
return 0;
}
/*
if a discordant read is mapped to MEI (overlap with MEI coord)
add centor of ( anchor_end + 3*avr_ins_var )
skip unmap & clip
check 3 types at the same time
*/
void Sites::AddDiscoverSiteFromSingleBam( SingleSampleInfo & si )
{
/*for(int i=0;i<NMEI; i++) {
std::cout << "m=" << i << ": ";
for(map<string, map<int, bool> >::iterator t=meiCoord[m].begin(); t!=meiCoord[m].end(); t++)
std::cout << t->first << "->" << t->second.size() << " ";
std::cout << std::endl;
}*/
avr_read_length = si.avr_read_length;
avr_ins_size = si.avr_ins_size;
min_read_length = avr_read_length / 3;
current_depth = si.depth;
// total_depth += current_depth;
resetDepthAddFlag();
SamFile bam;
SamFileHeader bam_header;
OpenBamAndBai( bam,bam_header, si.bam_name );
for( int i=0; i<pchr_list->size(); i++ ) {
string chr = (*pchr_list)[i];
// if ( !single_chr.empty() && chr.compare(single_chr)!=0 )
// continue;
if ( siteList.find(chr) == siteList.end() )
siteList[chr].clear();
// map<string, map<int, SingleSite> >::iterator pchr = siteList[m].find(chr);
// map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(chr);
// if (coord_chr_ptr == meiCoord[m].end())
// continue;
bool section_status;
if (range_start<0) { // no range
section_status = bam.SetReadSection( chr.c_str() );
if (!section_status) {
string str = "Cannot set read section at chr " + chr;
morphWarning( str );
}
}
else { // set range
section_status = bam.SetReadSection( chr.c_str(), range_start, range_end );
if (!section_status) {
string str = "Cannot set read section at chr " + chr + " " + std::to_string(range_start) + "-" + std::to_string(range_end);
morphWarning( str );
}
}
// DO ADDING
// if (siteList[chr].empty())
// p_reach_last = 1;
// else {
// p_reach_last = 0;
pnearest = siteList[chr].begin();
// }
SingleSite new_site; // temporary cluster. will be added to map later.
new_site.depth = current_depth;
bool start_new = 1; // check if need to add new_site to map and start new new_site
SamRecord rec;
int between = 0; // count #reads after new_site.end. If end changed, add it to rcount and reset to zero
while( bam.ReadRecord( bam_header, rec ) ) {
if (!start_new) {
if (rec.get1BasedPosition() >= new_site.end)
between++;
else
new_site.rcount++;
}
if (rec.getFlag() & 0x2)
continue;
if ( OneEndUnmap( rec.getFlag() ) )
continue;
if ( IsSupplementary(rec.getFlag()) )
continue;
if ( rec.getReadLength() < min_read_length )
continue;
if ( rec.getMapQuality() < MIN_QUALITY )
continue;
if (chr.compare(rec.getMateReferenceName())==0 && rec.getInsertSize() < abs(avr_ins_size*2))
continue;
bool is_mei = 0;
vector<bool> is_in_coord;
is_in_coord.resize(3, 0);
for(int m=0; m<NMEI; m++) {
map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(rec.getMateReferenceName());
if (coord_chr_ptr == meiCoord[m].end())
is_in_coord[m] = 0;
else
is_in_coord[m] = isWithinCoord( rec.get1BasedMatePosition(), coord_chr_ptr->second ); // within MEI coord
if (is_in_coord[m])
is_mei = 1;
}
if (!is_mei)
continue;
if (start_new) {
setNewCluster( is_in_coord, new_site,rec);
start_new = 0;
between = 0;
}
else { // add to existing cluster
if ( rec.get1BasedPosition() > new_site.end + avr_ins_size ) { // start new coord
addClusterToMap(new_site, siteList[chr]);
setNewCluster( is_in_coord, new_site, rec);
start_new = 0;
between = 0;
}
else {
addToCurrentCluster( is_in_coord, new_site, rec);
new_site.rcount += between;
between = 0;
}
}
}
// add last one
if (!start_new)
addClusterToMap(new_site, siteList[chr]);
}
bam.Close();
}