本文整理汇总了C++中SamFile::SetReadFlags方法的典型用法代码示例。如果您正苦于以下问题：C++ SamFile::SetReadFlags方法的具体用法？C++ SamFile::SetReadFlags怎么用？C++ SamFile::SetReadFlags使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类SamFile的用法示例。
在下文中一共展示了SamFile::SetReadFlags方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: execute
//.........这里部分代码省略.........
baseQCPtr = ifopen(pBaseQC, "w");
PileupElementBaseQCStats::setPercentStats(true);
}
else if(!cBaseQC.IsEmpty())
{
baseQCPtr = ifopen(cBaseQC, "w");
PileupElementBaseQCStats::setPercentStats(false);
}
if(baseQCPtr != NULL)
{
PileupElementBaseQCStats::setOutputFile(baseQCPtr);
PileupElementBaseQCStats::printHeader();
}
if((baseQCPtr != NULL) || baseSum)
{
PileupElementBaseQCStats::setMapQualFilter(minMapQual);
PileupElementBaseQCStats::setBaseSum(baseSum);
}
if(params)
{
inputParameters.Status();
}
// Open the file for reading.
SamFile samIn;
if(!samIn.OpenForRead(inFile))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}
samIn.SetReadFlags(requiredFlags, excludeFlags);
// Set whether or not basic statistics should be generated.
samIn.GenerateStatistics(basic);
// Read the sam header.
SamFileHeader samHeader;
if(!samIn.ReadHeader(samHeader))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}
// Open the bam index file for reading if we are
// doing unmapped reads (also set the read section).
if(useIndex)
{
samIn.ReadBamIndex(indexFile);
if(unmapped)
{
samIn.SetReadSection(-1);
}
if(!regionList.IsEmpty())
{
myRegionList = ifopen(regionList, "r");
}
}
//////////////////////////
// Read dbsnp if specified and doing baseQC
if(((baseQCPtr != NULL) || baseSum) && (!dbsnp.IsEmpty()))示例2: if
//.........这里部分代码省略.........
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)
{示例3: testFlagRead
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();
}