Fix a bug if using fasta file

mourisl · Jul 28, 2015 · 0281af9 · 0281af9
1 parent ae36a3a
commit 0281af9
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/ErrorCorrection.cpp b/ErrorCorrection.cpp
@@ -48,7 +48,7 @@ int CreateAnchor( char *read, char *qual, int *fix, bool *storedKmer, KmerCode &
  int kmerLength = kmerCode.GetKmerLength() ; 
  int i, j, k ;
  //if ( readLength < 2 * kmerLength )
- // return -1 ;
+  // return -1 ;
  int maxLen = 0 ;
  int maxLenStats[2] = {0, 0}; // 0-position, 1-which nucleutide changed to
 
@@ -146,7 +146,7 @@ int CreateAnchor( char *read, char *qual, int *fix, bool *storedKmer, KmerCode &
  //read[i] = c ;
  //break ;
  }
- else if ( max > 0 && max == maxLen && qual[i] < qual[ maxLenStats[0] ] )
+ else if ( max > 0 && max == maxLen && qual[0] != '\0' && qual[i] < qual[ maxLenStats[0] ] )
  {
  maxLenStats[0] = i ;
  maxLenStats[1] = j ;
@@ -921,14 +921,14 @@ int ErrorCorrection( char *read, char *qual, KmerCode& kmerCode, int maxCorrecti
  {
  if ( i >= kmerLength && ( fix[i - kmerLength] >= 0 && read[i - kmerLength] != 'N' ) )
  {
- if ( qual[i - kmerLength] <= badQuality )
+ if ( qual[0] != '\0' && qual[i - kmerLength] <= badQuality )
  correctCnt -= 0.5 ;
  else
  --correctCnt ;
  }
  if ( fix[i] >= 0 && read[i] != 'N' )
  {
- if ( qual[i] <= badQuality )
+ if ( qual[0] != '\0' && qual[i] <= badQuality )
  correctCnt += 0.5 ;
  else
  ++correctCnt ;