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| | === Usage Examples === | | === Usage Examples === |
| − | ==== Simple Read/Write SAM/BAM files ====
| + | [[Sam Library Usage Examples]] |
| − | 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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| − | | |
| − | <source lang="cpp">
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| − | #include "SamFile.h"
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| − | #include "SamValidation.h"
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| − | | |
| − | int main(int argc, char ** argv)
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| − | {
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| − | // Check for the appropriate number of arguments.
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| − | if(argc != 3)
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| − | {
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| − | printf("./bam <inputFile> <outputFile.sam/bam>\n");
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| − | exit(-1);
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| − | }
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| − | | |
| − | // Open the input file for reading.
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| − | SamFile samIn;
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| − | if(!samIn.OpenForRead(argv[1]))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Open the output file for writing.
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| − | SamFile samOut;
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| − | if(!samOut.OpenForWrite(argv[2]))
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| − | {
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | return(samOut.GetStatus());
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| − | }
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| − | | |
| − | // Read the sam header.
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| − | SamFileHeader samHeader;
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| − | if(!samIn.ReadHeader(samHeader))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Write the sam header.
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| − | if(!samOut.WriteHeader(samHeader))
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| − | {
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | return(samOut.GetStatus());
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| − | }
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| − | | |
| − | SamRecord samRecord;
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| − | SamValidationErrors samInvalidErrors;
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| − | | |
| − | // Set writeStatus to success. It will be changed
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| − | // to the failure reason if any of the writes fail.
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| − | SamStatus::Status writeStatus = SamStatus::SUCCESS;
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| − | | |
| − | // Keep reading records until ReadRecord returns false.
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| − | while(samIn.ReadRecord(samHeader, samRecord))
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| − | {
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| − | // Successfully read a record from the file, so write it.
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| − | if(!samOut.WriteRecord(samHeader, samRecord))
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| − | {
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| − | // Failed to write a record.
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | writeStatus = samOut.GetStatus();
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| − | }
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| − | }
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| − | | |
| − | if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
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| − | {
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| − | // Failed to read a record.
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | }
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| − | | |
| − | std::cout << std::endl << "Number of records read = " <<
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| − | samIn.GetCurrentRecordCount() << std::endl;
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| − | std::cout << "Number of records written = " <<
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| − | samOut.GetCurrentRecordCount() << std::endl;
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| − | | |
| − | if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
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| − | {
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| − | // Failed reading a record.
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Since the reads were successful, return the status based
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| − | // on the status of the writes. If any failed, return
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| − | // their failure status.
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| − | return(writeStatus);
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| − | }
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| − | </source>
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| − | | |
| − | | |
| − | ==== Simple Read/Write Indexed BAM Files ====
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| − | 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.
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| − | <source lang="cpp">
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| − | #include "SamFile.h"
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| − | #include "SamValidation.h"
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| − | | |
| − | int ReadIndexedBam(const char* inputFilename,
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| − | const char* outputFilename,
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| − | const char* indexFilename)
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| − | {
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| − | // Open the input file for reading.
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| − | SamFile samIn;
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| − | if(!samIn.OpenForRead(inputFilename))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Open the bam index file for reading.
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| − | if(!samIn.ReadBamIndex(indexFilename))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Open the output file for writing.
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| − | SamFile samOut;
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| − | if(!samOut.OpenForWrite(outputFilename))
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| − | {
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | return(samOut.GetStatus());
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| − | }
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| − | | |
| − | // Read the sam header.
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| − | SamFileHeader samHeader;
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| − | if(!samIn.ReadHeader(samHeader))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Write the sam header.
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| − | if(!samOut.WriteHeader(samHeader))
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| − | {
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | return(samOut.GetStatus());
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| − | }
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| − | | |
| − | SamRecord samRecord;
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| − | SamValidationErrors samInvalidErrors;
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| − | | |
| − | // Loop through each Reference.
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| − | for(int i = -1; i < 23; i++)
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| − | {
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| − | int numSectionRecords = 0;
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| − | samIn.SetReadSection(i);
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| − | // Keep reading records until they aren't more.
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| − | while(samIn.ReadRecord(samHeader, samRecord))
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| − | {
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| − | numSectionRecords++;
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| − | // Successfully read a record from the file, so write it.
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| − | if(!samOut.WriteRecord(samHeader, samRecord))
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| − | {
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| − | // Failed to write a record.
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| − | fprintf(stderr, "%s\n", samOut.GetStatusMessage());
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| − | }
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| − | }
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| − | | |
| − | if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
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| − | {
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| − | // Failed to read a record.
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | }
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| − | | |
| − | std::cout << "Reference ID " << i << " has " << numSectionRecords
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| − | << " records" << std::endl;
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| − | }
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| − |
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| − | std::cout << "Number of records = " << samIn.GetCurrentRecordCount() << std::endl;
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| − |
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| − | return(0);
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| − | }
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| − | </source>
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| − | | |
| − | ==== Validate SAM/BAM Files Continuing Processing After Allowed Errors ====
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| − | 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.
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| − | <source lang="cpp">
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| − | #include "SamFile.h"
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| − | #include "SamValidation.h"
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| − | | |
| − | int Validate(String inFile, int quitAfterErrorNum, int maxReportedErrors, SamFile::SortedType sortType)
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| − | {
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| − | // Check to see if the in file was specified. If it wasn't this is an error.
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| − | if(inFile == "")
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| − | {
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| − | // In file was not specified but it is mandatory.
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| − | std::cerr << "--in is a mandatory argument for validate, "
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| − | << "but was not specified" << std::endl;
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| − | return(-1);
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| − | }
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| − | | |
| − | SamFile samIn;
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| − | // Open the file for reading.
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| − | if(!samIn.OpenForRead(inFile))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Set the sorting validation type.
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| − | samIn.setSortedValidation(sortType);
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| − | | |
| − | // Read the sam header.
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| − | SamFileHeader samHeader;
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| − | if(!samIn.ReadHeader(samHeader))
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| − | {
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| − | fprintf(stderr, "%s\n", samIn.GetStatusMessage());
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| − | return(samIn.GetStatus());
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| − | }
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| − | | |
| − | // Read the sam records.
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| − | SamRecord samRecord;
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| − | | |
| − | // Track the status.
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| − | SamStatus::Status status = SamStatus::SUCCESS;
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| − | | |
| − | // Keep reading records until the end of the file is reached.
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| − | int numValidRecords = 0;
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| − | int numInvalidRecords = 0;
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| − | int numErrorRecords = 0;
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| − | int numRecords = 0;
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| − | int numReportedErrors = 0;
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| − | int totalErrorRecords = 0;
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| − | | |
| − | SamValidationErrors invalidSamErrors;
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| − | | |
| − | // Keep reading records from the file until SamFile::ReadRecord
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| − | // indicates to stop (returns false).
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| − | while( (samIn.ReadRecord(samHeader, samRecord))||
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| − | (SamStatus::isContinuableStatus(samIn.GetStatus()) &&
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| − | ( (quitAfterErrorNum < 0) ||
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| − | (numErrorRecords < quitAfterErrorNum) )) )
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| − | {
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| − | ++numRecords;
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| − | if(samIn.GetStatus() == SamStatus::SUCCESS)
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| − | {
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| − | // Successfully set the record, so check to see if it is valid.
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| − | // Clear any errors in the list.
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| − | invalidSamErrors.clear();
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| − | if(!SamValidator::isValid(samHeader, samRecord, invalidSamErrors))
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| − | {
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| − | // The record is not valid.
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| − | ++numInvalidRecords;
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| − | ++totalErrorRecords;
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| − | if(numReportedErrors < maxReportedErrors)
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| − | {
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| − | std::cout << "Record " << numRecords << std::endl
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| − | << invalidSamErrors << std::endl;
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| − | numReportedErrors += invalidSamErrors.numErrors();
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| − | status = SamStatus::INVALID;
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| − | }
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| − | }
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| − | else
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| − | {
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| − | // Valid record, so increment the counter.
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| − | ++numValidRecords;
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| − | }
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| − | }
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| − | else
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| − | {
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| − | // Error reading the record.
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| − | ++numErrorRecords;
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| − | if(numReportedErrors < maxReportedErrors)
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| − | {
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| − | // report error.
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| − | std::cout << "Record " << numRecords << std::endl
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| − | << samIn.GetStatusMessage() << std::endl
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| − | << std::endl;
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| − | ++numReportedErrors;
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| − | ++totalErrorRecords;
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| − | status = samIn.GetStatus();
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| − | }
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| − | }
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| − | }
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| − | | |
| − | if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
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| − | {
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| − | ++numErrorRecords;
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| − | // The last read call had a failure, so report it.
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| − | if(numReportedErrors < maxReportedErrors)
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| − | {
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| − | std::cout << "Record " << numRecords << ": ";
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| − | std::cout << std::endl << samIn.GetStatusMessage() << std::endl;
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| − | }
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| − | status = samIn.GetStatus();
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| − | }
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| − | | |
| − | printf("\nNumber of records read = %d\n", numRecords);
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| − | printf("Number of valid records = %d\n", numValidRecords);
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| − | printf("Returning: %d (%s)\n", status, SamStatus::getStatusString(status));
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| − | return(status);
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| − | }
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| − | </source>
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