Sam Library Usage Examples - Revision history

Mktrost: Remove unused code, add reference to BamUtil

2011-09-07T13:07:49Z

Remove unused code, add reference to BamUtil

← Older revision		Revision as of 09:07, 7 September 2011
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	= Usage Examples =		= Usage Examples =
	This page contains examples on how to use the [[C++ Library: libStatGen\|SAM/BAM Library]].		This page contains examples on how to use the [[C++ Library: libStatGen\|SAM/BAM Library]].

			See [[BamUtil]] for more examples of how it uses libStatGen to perform many operations.

	== Simple Read/Write SAM/BAM files ==		== Simple Read/Write SAM/BAM files ==
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	SamRecord samRecord;		SamRecord samRecord;
	~~SamValidationErrors samInvalidErrors;~~

	// Set returnStatus to success. It will be changed		// Set returnStatus to success. It will be changed
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	SamRecord samRecord;		SamRecord samRecord;
	~~SamValidationErrors samInvalidErrors;~~

	// Loop through each Reference.		// Loop through each Reference.

Mktrost at 17:41, 24 August 2011

2011-08-24T17:41:46Z

← Older revision		Revision as of 13:41, 24 August 2011
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	= Usage Examples =		= Usage Examples =
	This page contains examples on how to use the [[C++ Library: ~~libbam~~\|SAM/BAM Library]].		This page contains examples on how to use the [[C++ Library: libStatGen\|SAM/BAM Library]].

	== Simple Read/Write SAM/BAM files ==		== Simple Read/Write SAM/BAM files ==

Mktrost at 05:48, 2 November 2010

2010-11-02T05:48:39Z

← Older revision		Revision as of 01:48, 2 November 2010
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			[[Category:libStatGen]]
			[[Category:libStatGen BAM]]

	= Usage Examples =		= Usage Examples =
	This page contains examples on how to use the [[C++ Library: libbam\|SAM/BAM Library]].		This page contains examples on how to use the [[C++ Library: libbam\|SAM/BAM Library]].

Mktrost at 15:58, 8 October 2010

2010-10-08T15:58:27Z

Show changes

Mktrost at 14:42, 2 August 2010

2010-08-02T14:42:49Z

Show changes

Mktrost at 20:47, 10 June 2010

2010-06-10T20:47:38Z

← Older revision		Revision as of 16:47, 10 June 2010
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			= Usage Examples =
	This page contains examples on how to use the [[C++ Library: libbam\|SAM/BAM Library]].		This page contains examples on how to use the [[C++ Library: libbam\|SAM/BAM Library]].

Mktrost at 20:47, 10 June 2010

2010-06-10T20:47:11Z

← Older revision		Revision as of 16:47, 10 June 2010
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			This page contains examples on how to use the [[C++ Library: libbam\|SAM/BAM Library]].

	== Simple Read/Write SAM/BAM files ==		== Simple Read/Write SAM/BAM files ==
	The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.		The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.

Mktrost at 18:51, 10 June 2010

2010-06-10T18:51:28Z

← Older revision		Revision as of 14:51, 10 June 2010
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	SamValidationErrors samInvalidErrors;		SamValidationErrors samInvalidErrors;

	// Set ~~writeStatus~~ to success. It will be changed		// Set returnStatus to success. It will be changed
	// to the failure reason if any of the writes fail.		// to the failure reason if any of the writes fail.
	SamStatus::Status ~~writeStatus~~ = SamStatus::SUCCESS;		SamStatus::Status returnStatus = SamStatus::SUCCESS;

	// Keep reading records until ReadRecord returns false.		// Keep reading records until ReadRecord returns false.
	while(samIn.ReadRecord(samHeader, samRecord))		while(samIn.ReadRecord(samHeader, samRecord))
	{		{
	// Successfully read a record from the file, so write it.		// Successfully read a record from the file, so write it.
	if(!samOut.WriteRecord(samHeader, samRecord))		if(!samOut.WriteRecord(samHeader, samRecord))
	{		{
	// Failed to write a record.		// Failed to write a record.
	fprintf(stderr, "%s\n", samOut.GetStatusMessage());		fprintf(stderr, "%s\n", samOut.GetStatusMessage());
	~~writeStatus~~ = samOut.GetStatus();		returnStatus = samOut.GetStatus();
	}		}
	}		}

	if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)		if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
	{		{
	// Failed to read a record.		// Failed to read a record.
	fprintf(stderr, "%s\n", samIn.GetStatusMessage());		fprintf(stderr, "%s\n", samIn.GetStatusMessage());
	}		// Set the return status to the reason why
			// the read failed.
			returnStatus = samIn.GetStatus();
			}

	std::cout << std::endl << "Number of records read = " <<		std::cout << std::endl << "Number of records read = " <<
	samIn.GetCurrentRecordCount() << std::endl;		samIn.GetCurrentRecordCount() << std::endl;
	std::cout << "Number of records written = " <<		std::cout << "Number of records written = " <<
	samOut.GetCurrentRecordCount() << std::endl;		samOut.GetCurrentRecordCount() << std::endl;

	~~if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)~~		// Since the reads were successful, return the status based
	{		// on the status of the writes. If any failed, return
	~~// Failed reading a record.~~		// their failure status.
	~~return(samIn.GetStatus());~~		return(returnStatus);
	}		}

	// Since the reads were successful, return the status based
	// on the status of the writes. If any failed, return
	// their failure status.
	return(~~writeStatus~~);
	}
	</source>		</source>

Mktrost at 18:41, 10 June 2010

2010-06-10T18:41:01Z

← Older revision		Revision as of 14:41, 10 June 2010
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	==== Simple Read/Write SAM/BAM files ====		== Simple Read/Write SAM/BAM files ==
	The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.		The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.

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	==== Simple Read/Write Indexed BAM Files ====		== Simple Read/Write Indexed BAM Files ==
	This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1. It also prints a count of the number of records in each section.		This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1. It also prints a count of the number of records in each section.
	<source lang="cpp">		<source lang="cpp">
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	</source>		</source>

	==== Validate SAM/BAM Files Continuing Processing After Allowed Errors ====		== Validate SAM/BAM Files Continuing Processing After Allowed Errors ==
	This example demonstrates calling validation on a SAM/BAM file. It also demonstrates a more complicated read loop that continues until a configurable number of errors are hit.		This example demonstrates calling validation on a SAM/BAM file. It also demonstrates a more complicated read loop that continues until a configurable number of errors are hit.
	<source lang="cpp">		<source lang="cpp">

Mktrost: Created page with '==== Simple Read/Write SAM/BAM files ==== The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined b…'

2010-06-10T18:40:26Z

Created page with '==== Simple Read/Write SAM/BAM files ==== The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined b…'

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==== Simple Read/Write SAM/BAM files ====
The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.

<source lang="cpp">
#include "SamFile.h"
#include "SamValidation.h"

int main(int argc, char ** argv)
{
// Check for the appropriate number of arguments.
if(argc != 3)
{
printf("./bam <inputFile> <outputFile.sam/bam>\n");
exit(-1);
}

// Open the input file for reading.
SamFile samIn;
if(!samIn.OpenForRead(argv[1]))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}

// Open the output file for writing.
SamFile samOut;
if(!samOut.OpenForWrite(argv[2]))
{
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}

// 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;
SamValidationErrors samInvalidErrors;

// Set writeStatus to success. It will be changed
// to the failure reason if any of the writes fail.
SamStatus::Status writeStatus = SamStatus::SUCCESS;

// Keep reading records until ReadRecord returns false.
while(samIn.ReadRecord(samHeader, samRecord))
{
// Successfully read a record from the file, so write it.
if(!samOut.WriteRecord(samHeader, samRecord))
{
// Failed to write a record.
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
writeStatus = samOut.GetStatus();
}
}

if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed to read a record.
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
}

std::cout << std::endl << "Number of records read = " <<
samIn.GetCurrentRecordCount() << std::endl;
std::cout << "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
// on the status of the writes. If any failed, return
// their failure status.
return(writeStatus);
}
</source>

==== Simple Read/Write Indexed BAM Files ====
This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1. It also prints a count of the number of records in each section.
<source lang="cpp">
#include "SamFile.h"
#include "SamValidation.h"

int ReadIndexedBam(const char* inputFilename,
const char* outputFilename,
const char* indexFilename)
{
// Open the input file for reading.
SamFile samIn;
if(!samIn.OpenForRead(inputFilename))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}

// Open the bam index file for reading.
if(!samIn.ReadBamIndex(indexFilename))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}

// Open the output file for writing.
SamFile samOut;
if(!samOut.OpenForWrite(outputFilename))
{
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}

// 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;
SamValidationErrors samInvalidErrors;

// Loop through each Reference.
for(int i = -1; i < 23; i++)
{
int numSectionRecords = 0;
samIn.SetReadSection(i);
// Keep reading records until they aren't more.
while(samIn.ReadRecord(samHeader, samRecord))
{
numSectionRecords++;
// Successfully read a record from the file, so write it.
if(!samOut.WriteRecord(samHeader, samRecord))
{
// Failed to write a record.
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
}
}

if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed to read a record.
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
}

std::cout << "Reference ID " << i << " has " << numSectionRecords
<< " records" << std::endl;
}

std::cout << "Number of records = " << samIn.GetCurrentRecordCount() << std::endl;

return(0);
}
</source>

==== Validate SAM/BAM Files Continuing Processing After Allowed Errors ====
This example demonstrates calling validation on a SAM/BAM file. It also demonstrates a more complicated read loop that continues until a configurable number of errors are hit.
<source lang="cpp">
#include "SamFile.h"
#include "SamValidation.h"

int Validate(String inFile, int quitAfterErrorNum, int maxReportedErrors, SamFile::SortedType sortType)
{
// Check to see if the in file was specified. If it wasn't this is an error.
if(inFile == "")
{
// In file was not specified but it is mandatory.
std::cerr << "--in is a mandatory argument for validate, "
<< "but was not specified" << std::endl;
return(-1);
}

SamFile samIn;
// Open the file for reading.
if(!samIn.OpenForRead(inFile))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}

// Set the sorting validation type.
samIn.setSortedValidation(sortType);

// Read the sam header.
SamFileHeader samHeader;
if(!samIn.ReadHeader(samHeader))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}

// Read the sam records.
SamRecord samRecord;

// Track the status.
SamStatus::Status status = SamStatus::SUCCESS;

// Keep reading records until the end of the file is reached.
int numValidRecords = 0;
int numInvalidRecords = 0;
int numErrorRecords = 0;
int numRecords = 0;
int numReportedErrors = 0;
int totalErrorRecords = 0;

SamValidationErrors invalidSamErrors;

// Keep reading records from the file until SamFile::ReadRecord
// indicates to stop (returns false).
while( (samIn.ReadRecord(samHeader, samRecord))||
(SamStatus::isContinuableStatus(samIn.GetStatus()) &&
( (quitAfterErrorNum < 0) ||
(numErrorRecords < quitAfterErrorNum) )) )
{
++numRecords;
if(samIn.GetStatus() == SamStatus::SUCCESS)
{
// Successfully set the record, so check to see if it is valid.
// Clear any errors in the list.
invalidSamErrors.clear();
if(!SamValidator::isValid(samHeader, samRecord, invalidSamErrors))
{
// The record is not valid.
++numInvalidRecords;
++totalErrorRecords;
if(numReportedErrors < maxReportedErrors)
{
std::cout << "Record " << numRecords << std::endl
<< invalidSamErrors << std::endl;
numReportedErrors += invalidSamErrors.numErrors();
status = SamStatus::INVALID;
}
}
else
{
// Valid record, so increment the counter.
++numValidRecords;
}
}
else
{
// Error reading the record.
++numErrorRecords;
if(numReportedErrors < maxReportedErrors)
{
// report error.
std::cout << "Record " << numRecords << std::endl
<< samIn.GetStatusMessage() << std::endl
<< std::endl;
++numReportedErrors;
++totalErrorRecords;
status = samIn.GetStatus();
}
}
}

if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
++numErrorRecords;
// The last read call had a failure, so report it.
if(numReportedErrors < maxReportedErrors)
{
std::cout << "Record " << numRecords << ": ";
std::cout << std::endl << samIn.GetStatusMessage() << std::endl;
}
status = samIn.GetStatus();
}

printf("\nNumber of records read = %d\n", numRecords);
printf("Number of valid records = %d\n", numValidRecords);
printf("Returning: %d (%s)\n", status, SamStatus::getStatusString(status));
return(status);
}
</source>