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C++ Class: SamFile (view source)

Revision as of 14:57, 11 May 2010

1,105 bytes added ,  14:57, 11 May 2010
no edit summary
Line 72: Line 72:  
| Get the Status Message of the last call that sets status.
 
| Get the Status Message of the last call that sets status.
 
|-
 
|-
−
| '''DEPRECATED: <code>SamStatus::Status SamFile::GetFailure()</code>'''
+
| '''DEPRECATED: '''<code>SamStatus::Status SamFile::GetFailure()</code>
 
| Get the type of failure that occurred on a method failure.
 
| Get the type of failure that occurred on a method failure.
 
|-
 
|-
Line 105: Line 105:     
<source lang="cpp">
 
<source lang="cpp">
 +
#include "SamFile.h"
 +
#include "SamValidation.h"
 +
 
int main(int argc, char ** argv)
 
int main(int argc, char ** argv)
 
{
 
{
 +
  // Check for the appropriate number of arguments.
 
   if(argc != 3)
 
   if(argc != 3)
 
   {
 
   {
Line 113: Line 117:  
   }
 
   }
   −
 
+
  // Open the input file for reading.
 
   SamFile samIn;
 
   SamFile samIn;
−
     
+
   if(!samIn.OpenForRead(argv[1]))
−
   samIn.OpenForRead(argv[1]);
+
  {
 +
      fprintf(stderr, "%s\n", samIn.GetStatusMessage());
 +
      return(samIn.GetStatus());
 +
  }
    +
  // Open the output file for writing.
 
   SamFile samOut;
 
   SamFile samOut;
−
 
+
   if(!samOut.OpenForWrite(argv[2]))
−
   samOut.OpenForWrite(argv[2]);
+
  {
 +
      fprintf(stderr, "%s\n", samOut.GetStatusMessage());
 +
      return(samOut.GetStatus());
 +
  }
    
   // Read the sam header.
 
   // Read the sam header.
 
   SamFileHeader samHeader;
 
   SamFileHeader samHeader;
−
   samIn.ReadHeader(samHeader);
+
   if(!samIn.ReadHeader(samHeader))
 +
  {
 +
      fprintf(stderr, "%s\n", samIn.GetStatusMessage());
 +
      return(samIn.GetStatus());
 +
  }
   −
   samOut.WriteHeader(samHeader);
+
   // Write the sam header.
 +
  if(!samOut.WriteHeader(samHeader))
 +
  {
 +
      fprintf(stderr, "%s\n", samOut.GetStatusMessage());
 +
      return(samOut.GetStatus());    
 +
  }
   −
  // Read the first sam record.
   
   SamRecord samRecord;
 
   SamRecord samRecord;
 +
  SamValidationErrors samInvalidErrors;
   −
   // Track if any of the records are invalid.  Initialize to 0, it will  
+
   // Set writeStatus to success.  It will be changed
−
   // be set to -1 on an invalid record.
+
   // to the failure reason if any of the writes fail.
−
   int status = 0;
+
   SamStatus::Status writeStatus = SamStatus::SUCCESS;
   −
   // Keep reading records until the end of the file is reached.
+
   // Keep reading records until ReadRecord returns false.
−
  int numValidRecords = 0;
+
   while(samIn.ReadRecord(samHeader, samRecord))
−
   while(!samIn.IsEOF())
   
   {
 
   {
−
       if(samIn.ReadRecord(samHeader, samRecord) == true)
+
      // Successfully read a record from the file, so write it.
 +
       if(!samOut.WriteRecord(samHeader, samRecord))
 
       {
 
       {
−
         // Successfully read a record from the file, so check to see
+
         // Failed to write a record.
−
        // if it is valid.
+
         fprintf(stderr, "%s\n", samOut.GetStatusMessage());
−
         if(samRecord.isValid(samHeader))
+
         writeStatus = samOut.GetStatus();
−
        {
  −
            //  It is valid, so write it.
  −
            numValidRecords++;
  −
            samOut.WriteRecord(samHeader, samRecord);
  −
         }
  −
        else
  −
        {
  −
            // There is at least one invalid record, return -1.
  −
            status = -1;
  −
        }
  −
      }
  −
      else
  −
      {
  −
        // Failed to read the record.  Check to see if it failed due to
  −
        // there being no more records, which is not a failure.  Any
  −
        // other failure reason counts as a failure.
  −
        if(samIn.GetFailure() != SamStatus::NO_MORE_RECS)
  −
        {
  −
            // Read failed, invalid.
  −
            status = -1;
  −
        }
   
       }
 
       }
 
   }
 
   }
−
   std::cout << "Number of records read = " <<  
+
 
 +
  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;
 
       samIn.GetCurrentRecordCount() << std::endl;
 
   std::cout << "Number of records written = " <<  
 
   std::cout << "Number of records written = " <<  
 
       samOut.GetCurrentRecordCount() << std::endl;
 
       samOut.GetCurrentRecordCount() << std::endl;
−
  std::cout << "Number of valid records = " << numValidRecords << std::endl;
     −
   return(status);
+
   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>
 
</source>
Line 184: Line 198:  
                   const char* indexFilename)
 
                   const char* indexFilename)
 
{
 
{
 +
  // Open the input file for reading.
 
   SamFile samIn;
 
   SamFile samIn;
−
     
+
   if(!samIn.OpenForRead(inputFilename))
−
   samIn.OpenForRead(inputFilename);
+
  {
−
   samIn.ReadBamIndex(indexFilename);
+
      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;
 
   SamFile samOut;
−
 
+
   if(!samOut.OpenForWrite(outputFilename))
−
   samOut.OpenForWrite(outputFilename);
+
  {
 +
      fprintf(stderr, "%s\n", samOut.GetStatusMessage());
 +
      return(samOut.GetStatus());
 +
  }
    
   // Read the sam header.
 
   // Read the sam header.
 
   SamFileHeader samHeader;
 
   SamFileHeader samHeader;
−
   samIn.ReadHeader(samHeader);
+
   if(!samIn.ReadHeader(samHeader))
 +
  {
 +
      fprintf(stderr, "%s\n", samIn.GetStatusMessage());
 +
      return(samIn.GetStatus());
 +
  }
 +
 
 
   // Write the sam header.
 
   // Write the sam header.
−
   samOut.WriteHeader(samHeader);
+
   if(!samOut.WriteHeader(samHeader))
 +
  {
 +
      fprintf(stderr, "%s\n", samOut.GetStatusMessage());
 +
      return(samOut.GetStatus());    
 +
  }
    
   SamRecord samRecord;
 
   SamRecord samRecord;
−
    
+
   SamValidationErrors samInvalidErrors;
−
  int numValidRecords = 0;
  −
  int numRecords = 0;
      
   // Loop through each Reference.
 
   // Loop through each Reference.
Line 209: Line 244:  
       int numSectionRecords = 0;
 
       int numSectionRecords = 0;
 
       samIn.SetReadSection(i);
 
       samIn.SetReadSection(i);
−
       // Keep reading records until they aren't read successfully.
+
       // Keep reading records until they aren't more.
−
       while(samIn.ReadRecord(samHeader, samRecord) == true)
+
       while(samIn.ReadRecord(samHeader, samRecord))
 
       {
 
       {
 
         numSectionRecords++;
 
         numSectionRecords++;
−
        numRecords++;
+
         // Successfully read a record from the file, so write it.
−
         // Successfully read a record from the file, so check to see
+
         if(!samOut.WriteRecord(samHeader, samRecord))
−
        // if it is valid.
  −
         if(samRecord.isValid(samHeader))
   
         {
 
         {
−
             // It is valid, so write it.
+
             // Failed to write a record.
−
             numValidRecords++;
+
             fprintf(stderr, "%s\n", samOut.GetStatusMessage());
−
            samOut.WriteRecord(samHeader, samRecord);
   
         }
 
         }
 
       }
 
       }
 +
 +
      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  
 
       std::cout << "Reference ID " << i << " has " << numSectionRecords  
 
                 << " records" << std::endl;
 
                 << " records" << std::endl;
 
   }
 
   }
−
     
+
 
−
   std::cout << "Number of records = " << numRecords << std::endl;
+
   std::cout << "Number of records = " << samIn.GetCurrentRecordCount() << std::endl;
−
   std::cout << "Number of valid records = " << numValidRecords << std::endl;
+
    
−
 
   
   return(0);
 
   return(0);
 
}
 
}
 
</source>
 
</source>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1299"

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