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ErrorCorrection.cpp
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ErrorCorrection.cpp
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#include "ErrorCorrection.h"
#include <string.h>
//#define DEBUG
extern char nucToNum[26] ;
extern char numToNuc[26] ;
extern int MAX_CORRECTION ;
extern bool ALLOW_TRIMMING ;
extern int SET_NEW_QUAL ;
void *ErrorCorrection_Thread( void *arg )
{
int ind ;
int correction, badPrefix, badSuffix, info ;
struct _ErrorCorrectionThreadArg *myArg = ( struct _ErrorCorrectionThreadArg *)arg ;
bool init = true ;
KmerCode kmerCode( myArg->kmerLength ) ;
while ( 1 )
{
pthread_mutex_lock( myArg->lock ) ;
if ( !init )
++myArg->batchFinished ;
ind = myArg->batchUsed ;
++myArg->batchUsed ;
pthread_mutex_unlock( myArg->lock ) ;
//printf( "%d %d\n", ind, myArg->batchSize ) ;
if ( ind >= myArg->batchSize )
break ;
correction = ErrorCorrection_Wrapper( myArg->readBatch[ind].seq, myArg->readBatch[ind].qual, kmerCode,
myArg->badQuality, myArg->trustedKmers, badPrefix, badSuffix, info ) ;
myArg->readBatch[ind].correction = correction ;
myArg->readBatch[ind].badPrefix = badPrefix ;
myArg->readBatch[ind].badSuffix = badSuffix ;
myArg->readBatch[ind].info = info ;
init = false ;
}
pthread_exit( NULL ) ;
return NULL ;
}
// If we could not find an anchor, it is mostly likely there are errors in every kmer.
// We will try to find 1 position that can create a stretch of stored kmers.
// return-which position is changed. -1: failed
int CreateAnchor( char *read, char *qual, int *fix, bool *storedKmer, KmerCode &kmerCode, Store *kmers )
{
int readLength = strlen( read ) ;
int kmerLength = kmerCode.GetKmerLength() ;
int i, j, k ;
//if ( readLength < 2 * kmerLength )
// return -1 ;
int maxLen = 0 ;
int maxLenStats[2] = {0, 0}; // 0-position, 1-which nucleutide changed to
// This stored the partial result of substitution, we use two arrays
// to keep the result for the optimal plan.
int tag = 0 ;
int stored[2][MAX_READ_LENGTH] ;
int scnt = 0 ;
int start = readLength / 2 - kmerLength ;
int end = readLength / 2 + kmerLength + 1 ;
/*if ( start < 0 )
start = 0 ;
if ( end > readLength )
end = readLength ;*/
start = 0 ;
end = readLength ;
for ( i = start ; i < end ; ++i )
{
int from = i - kmerLength + 1 ;
if ( from < 0 )
from = 0 ;
for ( j = 0 ; j < 4 ; ++j )
{
if ( numToNuc[j] == read[i] )
continue ;
char c = read[i] ;
read[i] = numToNuc[j] ;
// For efficiency, use one kmer to test whether we want to choose this candidate
// But for bigger kmer, we need more effort
// kind of test 1/32 of the kmers. Since the sequencing error are less likely on left-side,
// we shift more on left
int loop = ( kmerLength - 1 ) / 32 + 1 ;
int t ;
for ( t = 0 ; t < loop ; ++t )
{
int l = i - ( 2 * loop - t - 1 ) * kmerLength / ( 2 * loop ) + 1 ;
if ( l < 0 )
l = 0 ;
if ( l + kmerLength - 1 >= readLength )
l = readLength - 1 - kmerLength + 1 ;
kmerCode.Restart() ;
for ( k = l ; k <= l + kmerLength - 1 ; ++k )
kmerCode.Append( read[k] ) ;
if ( kmers->IsIn( kmerCode ) )
{
break ;
}
}
if ( t >= loop )
{
read[i] = c ;
continue ;
}
scnt = 0 ;
for ( k = from ; k < from + kmerLength - 1 ; ++k )
kmerCode.Append( read[k] ) ;
scnt = 0 ;
int missCnt = 0 ;
int hitCnt = 0 ;
for ( ; k < readLength && k < i + kmerLength ; ++k, ++scnt )
{
kmerCode.Append( read[k] ) ;
if ( kmers->IsIn( kmerCode ) )
{
stored[tag][scnt] = 1 ;
++hitCnt ;
}
else
{
stored[tag][scnt] = 0 ;
++missCnt ;
if ( kmerLength - missCnt < maxLen )
break ;
}
}
int sum = 0 ;
int max = 0 ;
for ( k = 0 ; k < scnt ; ++k )
{
if ( stored[tag][k] == 0 )
{
if ( sum > max )
max = sum ;
sum = 0 ;
}
else
++sum ;
}
if ( sum > max )
max = sum ;
if ( max > maxLen )
{
maxLen = max ;
maxLenStats[0] = i ;
maxLenStats[1] = j ;
/*for ( int l = 0 ; l < scnt ; ++l )
printf( "%d ", stored[tag][l] ) ;
printf( "\n" ) ;*/
tag = 1 - tag ;
//read[i] = c ;
//break ;
}
else if ( max > 0 && max == maxLen && qual[0] != '\0' && qual[i] < qual[ maxLenStats[0] ] )
{
maxLenStats[0] = i ;
maxLenStats[1] = j ;
tag = 1 - tag ;
}
read[i] = c ;
}
}
if ( maxLen == 0 )
{
//printf( "%s\n", read ) ;
return -1 ;
}
// Pass the effect of substitution
fix[ maxLenStats[0] ] = maxLenStats[1] ;
i = maxLenStats[0] ;
//printf( "%d: %d %d\n", maxLen, i, maxLenStats[1] ) ;
int from = i - kmerLength + 1 ;
if ( from < 0 )
from = 0 ;
for ( j = 0, k = from ; k + kmerLength - 1 < readLength && k <= i ; ++k, ++j )
{
//printf( "%d %d %d\n", j, k, stored[1 - tag][j] ) ;
storedKmer[k] = ( stored[1 - tag][j] == 1 ) ? true : false ;
}
return maxLenStats[0] ;
}
int ErrorCorrection( char *read, char *qual, KmerCode& kmerCode, int maxCorrection, char badQuality, Store *kmers, int &badPrefix, int &badSuffix, int &info )
{
int i, j, k ;
bool storedKmer[MAX_READ_LENGTH] ;
int kmerCnt = 0 ;
int readLength = 0 ;
int fix[MAX_READ_LENGTH] ; // The fixed character for each untrusted position.
bool trusted[MAX_READ_LENGTH] ; // Do not correct these makred positions.
int tag ;
int from, to ;
int trimStart = -1 ;
int ambiguousCnt = 0 ;
int alternativeCnt = 0 ;
bool hasAnchor = false ;
int createAnchorPos = -1 ;
bool noCandidateKmer = false ;
// KmerCode kmerCode( inCode ) ;
KmerCode tmpKmerCode( 0 ) ;
badPrefix = badSuffix = 0 ;
info = 0 ;
int kmerLength = kmerCode.GetKmerLength() ;
kmerCode.Restart() ;
for ( i = 0 ; i < kmerLength && read[i] ; ++i )
{
kmerCode.Append( read[i] ) ;
}
if ( !kmers->IsIn( kmerCode ) )
storedKmer[0] = false ;
else
{
storedKmer[0] = true ;
hasAnchor = true ;
}
kmerCnt = 1 ;
for ( ; read[i] ; ++i, ++kmerCnt )
{
kmerCode.Append( read[i] ) ;
if ( !kmers->IsIn( kmerCode ) )
storedKmer[ kmerCnt ] = false ;
else
{
storedKmer[ kmerCnt ] = true ;
hasAnchor = true ;
}
}
readLength = i ;
if ( readLength < kmerLength )
return 0 ;
trimStart = readLength ;
for ( i = 0 ; i < readLength ; ++i )
fix[i] = -1 ;
for ( i = 0 ; i < readLength ; ++i )
trusted[i] = false ;
tag = -1 ;
for ( i = 0 ; i < kmerCnt ; ++i )
{
if ( storedKmer[i] )
{
if ( tag == -1 )
tag = i ;
}
else
{
if ( tag != -1 )// && i - tag >= 3 )
{
for ( j = tag ; j < i + kmerLength - 1 ; ++j )
trusted[j] = true ;
}
tag = -1 ;
}
}
if ( !hasAnchor )
{
createAnchorPos = CreateAnchor( read, qual, fix, storedKmer, kmerCode, kmers ) ;
if ( createAnchorPos == -1 )
{
info = 3 ;
return -1 ;
}
++alternativeCnt ;
}
//printf( "%d %d %d\n", kmerLength, kmerCnt, i ) ;
#ifdef DEBUG
printf( "%s\n", read ) ;
for ( i = 0 ; i < kmerCnt ; ++i )
printf( "%d", storedKmer[i] ) ;
printf( "\n" ) ;
#endif
//exit( 1 ) ;
// All the kmers are reliable.
for ( i = 0 ; i < kmerCnt ; ++i )
{
if ( storedKmer[i] == false )
break ;
}
/*if ( !strcmp( read, "TTGCGTAAGATGGGGGTACCCACGTGGTGTCAGAGTGTCTCTCATTTCGGTTTGATCTACGCAGATCTACAAAAAATGCGGGAGAATAGACGCAGAGTTCT" ) )
{
printf( "## %d\n", i ) ;
exit( 1 ) ;
}*/
if ( i >= kmerCnt )
return 0 ;
// Find the first trusted kmer
int longestStoredKmerCnt = 0, storedKmerCnt = 0 ;
tag = -1 ;
for ( i = 0 ; i < kmerCnt ; ++i )
{
if ( storedKmer[i] )
{
++storedKmerCnt ;
}
else
{
if ( storedKmerCnt > longestStoredKmerCnt )
{
longestStoredKmerCnt = storedKmerCnt ;
tag = i - storedKmerCnt ;
}
storedKmerCnt = 0 ;
}
}
if ( storedKmerCnt > longestStoredKmerCnt )
{
longestStoredKmerCnt = storedKmerCnt ;
tag = i - storedKmerCnt ;
}
if ( longestStoredKmerCnt == 0 )
{
info = 3 ;
return -1 ;
}
if ( longestStoredKmerCnt >= kmerCnt )
{
//printf( "0%s\n", read ) ;
return 0 ;
}
//if ( tag > 0 )
// return 0 ;
for ( k = tag + 1 ; k < kmerCnt ; ++k )
if ( !storedKmer[k] )
break ;
// Scan towards right
kmerCode.Restart() ;
if ( k >= kmerCnt )
// The kmers are all correct after tag, so force skip the correction.
i = readLength + 1 ;
else
{
char backupC = '\0' ;
if ( createAnchorPos != -1 )
{
backupC = read[ createAnchorPos ] ;
read[ createAnchorPos ] = numToNuc[ fix[ createAnchorPos ] ] ;
}
if ( longestStoredKmerCnt < kmerLength )
{
for ( i = k - 1 + 1 ; i < k - 1 + kmerLength - 1 + 1 ; ++i )
{
kmerCode.Append( read[i] ) ;
}
}
else
{
// Adjust the anchor if necessary
// Test whether the current anchor is good
for ( i = k ; i < k + kmerLength ; ++i )
kmerCode.Append( read[i] ) ;
int c ;
for ( c = 0 ; c < 4 ; ++c )
{
if ( numToNuc[c] == read[i - 1] )
continue ;
if ( numToNuc[c] == read[i - 1] )
continue ;
tmpKmerCode = kmerCode ;
tmpKmerCode.ShiftRight() ;
tmpKmerCode.Append( numToNuc[c] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
{
// Test whether this branch makes sense
int t = 0 ;
for ( t = 0 ; t < kmerLength && read[i + t] ; ++t ) // and it is should be a very good fix
{
tmpKmerCode.Append( read[i + t] ) ;
if ( !kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( !read[i + t] || t >= kmerLength )
break ;
}
}
if ( c < 4 )
{
//kmerCode.ShiftRight( 1 ) ; Seems wrong
for ( i = k - 1 ; i < k + kmerLength - 1 ; ++i )
kmerCode.Append( read[i] ) ;
}
else
{
// Adjust the right side
for ( j = kmerLength / 2 - 1 ; j >= 0 ; --j )
{
int c ;
KmerCode tmpKmerCode( kmerLength ) ;
for ( i = k - j - 1 ; i < k - j + kmerLength - 1 ; ++i )
kmerCode.Append( read[i] ) ;
//printf( "%d %d %c\n", j, i, read[i - 1] ) ;
for ( c = 0 ; c < 4 ; ++c )
{
if ( numToNuc[c] == read[i - 1] )
continue ;
tmpKmerCode = kmerCode ;
tmpKmerCode.ShiftRight() ;
tmpKmerCode.Append( numToNuc[c] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
{
++alternativeCnt ;
// Test whether this branch makes sense
int t = 0 ;
for ( t = 0 ; t <= kmerLength / 2 && read[i + t] ; ++t ) // and it is should be a very good fix
{
tmpKmerCode.Append( read[i + t] ) ;
if ( !kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( t > kmerLength / 2 )
break ;
}
}
if ( c < 4 )
{
// adjust the anchor
--i ;
kmerCode.ShiftRight() ;
break ;
}
}
}
}
if ( createAnchorPos != -1 )
{
read[ createAnchorPos ] = backupC ;
}
}
/*for ( i = k ; i < k + kmerLength - 1 ; ++i )
{
kmerCode = ( kmerCode << (uint64_t)2 ) & mask ;
kmerCode = kmerCode | (uint64_t)nucToNum[ read[i] - 'A' ] ;
}*/
for ( ; i < readLength ; )
{
KmerCode fixedKmerCode( kmerCode ) ;
int maxTo = -1 ;
int maxChange = -1 ;
int maxCnt = 0 ;
int testCnt = 0 ;
from = i + 1 ;
to = ( i + kmerLength - 1 < readLength ) ? i + kmerLength - 1 : readLength - 1 ;
for ( j = 0 ; j < 4 ; ++j )
{
//kmerCode = ( fixedKmerCode << (uint64_t)2 ) & mask ;
//kmerCode = kmerCode | (uint64_t)j ;
kmerCode = fixedKmerCode ;
kmerCode.Append( numToNuc[j] ) ;
//printf( "?code=%llu\n", kmerCode.GetCode() ) ;
if ( !kmers->IsIn( kmerCode ) )
continue ;
if ( maxTo == -1 )
maxTo = i ;
++testCnt ;
// How many kmers this change can fix
for ( k = from ; k <= to ; ++k )
{
kmerCode.Append( read[k] ) ;
if ( !kmers->IsIn( kmerCode ) )
break ;
}
// Try to extend 1 position
if ( k > to && to == readLength - 1 )
{
int l, m ;
for ( m = 0 ; m < kmerLength - 1 - ( to - from + 1 ) ; ++m )
{
for ( l = 0 ; l < 4 ; ++l )
{
KmerCode tmpKmerCode( kmerCode ) ;
tmpKmerCode.Append( numToNuc[l] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( l < 4 )
{
//printf( "hi\n" ) ;
kmerCode.Append( numToNuc[l] ) ;
++k ;
}
}
}
//printf( "hi %d %d\n", k, maxTo ) ;
if ( k > maxTo )
{
/*if ( maxTo - from + 1 >= kmerLength / 2 )
{
++maxCnt ;
}
else*/
maxCnt = 1 ;
maxTo = k ;
maxChange = j ;
tmpKmerCode = kmerCode ;
}
/*else if ( k - from + 1 >= kmerLength / 2 )
{
++maxCnt ;
}*/
else if ( k == maxTo )
{
++maxCnt ;
if ( k == i + 1 && j == nucToNum[ read[i] - 'A' ] )
{
maxCnt = 1 ;
maxChange = j ;
tmpKmerCode = kmerCode ;
}
else if ( k == i + 1 && maxChange == nucToNum[ read[i] - 'A' ] )
{
maxCnt = 1 ;
}
}
//printf( "%d\n", j ) ;
}
#ifdef DEBUG
printf( "+hi %d: %d %d=>%d, (%d)\n", i, maxTo, to, maxChange, maxCnt ) ;
#endif
if ( testCnt > 1 )
alternativeCnt += ( testCnt - 1 ) ;
// TODO: if maxTo is far from i, then we may in a repeat. Try keep this base unfixed
// see whether the next fixing makes sense.
if ( maxTo == -1 || ( maxCnt > 1 && ( maxTo <= to || to - i + 1 < kmerLength ) ) )
{
//printf( "+%s\n", read ) ;
// trim
//if ( maxCnt > 1 )
//{
if ( maxTo == -1 )
noCandidateKmer = true ;
trimStart = i ;
info = 2 ;
break ;
//}
//else
//return 0 ;
}
fix[i] = maxChange ;
if ( maxCnt > 1 )
{
// Remove the effect of the ambiguous fixing
fix[i] = -2 ;
++ambiguousCnt ;
}
if ( maxTo >= readLength )
break ;
if ( maxTo <= to )
{
// There are multiple errors in the region
if ( 0 ) //maxTo > i + 1 )
{
// The next start search can start one place earlier
//uint64_t tmp ;
/*kmerCode.ShiftRi ;
if ( fix[maxTo - kmerLength + 1] != -1 )
kmerCode |= ( (uint64_t)fix[maxTo - kmerLength + 1] << ( 2ull * ( kmerLength - 2 ) ) ) ;
else
kmerCode |= ( (uint64_t)nucToNum[ read[maxTo - kmerLength + 1] - 'A' ] << ( 2ull * ( kmerLength -2 ) ) ) ;
i = maxTo - 1 ;*/
}
else
{
kmerCode = tmpKmerCode ;
kmerCode.ShiftRight() ;
i = maxTo ;
}
continue ;
}
else
{
// Search for next error.
for ( k = to - kmerLength + 2 ; k < kmerCnt ; ++k )
if ( !storedKmer[k] )
break ;
if ( k >= kmerCnt )
break ;
kmerCode.Restart() ;
for ( i = k - 1 + 1 ; i < k - 1 + kmerLength - 1 + 1 ; ++i )
{
if ( fix[i] < 0 )
kmerCode.Append( read[i] ) ;
else
kmerCode.Append( numToNuc[ fix[i] ] ) ;
}
continue ;
}
}
// Scan towards left
//printf( "%d\n", tag ) ;
if ( tag == 0 )
{
// Force skip
tag = -1 ;
}
else
{
char backupC = '\0' ;
if ( createAnchorPos != -1 )
{
backupC = read[ createAnchorPos ] ;
read[ createAnchorPos ] = numToNuc[ fix[ createAnchorPos ] ] ;
}
if ( longestStoredKmerCnt < kmerLength )
{
kmerCode.Restart() ;
for ( i = tag + 1 - 1 ; i < tag + kmerLength - 1 ; ++i )
{
kmerCode.Append( read[i] ) ;
}
kmerCode.Append( 'A' ) ;
}
else
{
// Test whether the current anchor is good
int c ;
j = -1 ;
for ( i = tag -1 ; i < tag - 1 + kmerLength ; ++i )
kmerCode.Append( read[i] ) ;
for ( c = 0 ; c < 4 ; ++c )
{
if ( numToNuc[c] == read[tag + j] )
continue ;
tmpKmerCode = kmerCode ;
tmpKmerCode.Append( 'A' ) ;
tmpKmerCode.Prepend( numToNuc[c] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
{
// Test whether this branch makes sense
int t = 0 ;
for ( t = 0 ; t <= kmerLength - 1 && tag + j - t - 1 >= 0 ; ++t ) // and it is should be a very good fix
{
tmpKmerCode.Prepend( read[tag + j - t - 1] ) ;
if ( !kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( t > kmerLength - 1 || tag + j -t -1 < 0 )
break ;
}
}
if ( c < 4 )
{
j = 0 ;
kmerCode.Restart() ;
for ( i = tag + j ; i < tag + j + kmerLength ; ++i )
kmerCode.Append( read[i] ) ;
}
else
{
// Adjust the left side of the anchor
for ( j = kmerLength / 2 - 1 ; j >= 0 ; --j )
{
int c ;
KmerCode tmpKmerCode( kmerLength ) ;
kmerCode.Restart() ;
for ( i = tag + j ; i < tag + j + kmerLength ; ++i )
kmerCode.Append( read[i] ) ;
//printf( "%d %d %c\n", j, i, read[i - 1] ) ;
for ( c = 0 ; c < 4 ; ++c )
{
if ( numToNuc[c] == read[tag + j] )
continue ;
tmpKmerCode = kmerCode ;
tmpKmerCode.Append( 'A' ) ;
tmpKmerCode.Prepend( numToNuc[c] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
{
++alternativeCnt ;
// Test whether this branch makes sense
int t = 0 ;
for ( t = 0 ; t <= kmerLength / 2 && tag + j - t - 1 >= 0 ; ++t ) // and it is should be a very good fix
{
tmpKmerCode.Prepend( read[tag + j - t - 1] ) ;
if ( !kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( t > kmerLength / 2 )
break ;
}
}
if ( c < 4 )
{
// adjust the anchor
tag = tag + j + 1 ;
kmerCode.Append( 'A' ) ;
break ;
}
}
}
}
if ( createAnchorPos != -1 )
{
read[ createAnchorPos ] = backupC ;
}
}
//kmerCode = ( kmerCode << (uint64_t)2 ) & mask ;
for ( i = tag - 1 ; i >= 0 ; )
{
KmerCode fixedKmerCode( kmerCode ) ;
int minTo = readLength + 1 ;
int minChange = -1 ;
int minCnt = 0 ;
int testCnt = 0 ;
from = i - 1 ;
to = ( i - kmerLength + 1 < 0 ) ? 0 : ( i - kmerLength + 1 ) ;
for ( j = 0 ; j < 4 ; ++j )
{
//kmerCode = ( fixedKmerCode >> (uint64_t)2 ) & ( mask >> 2ull ) ;
//printf( "1.%llu\n", kmerCode.GetCode() ) ;
//kmerCode = kmerCode | ( ((uint64_t)j) << (uint64_t)(2 * kmerLength - 2 ) ) ;
kmerCode = fixedKmerCode ;
kmerCode.Prepend( numToNuc[j] ) ;
//printf( "2.%llu\n", kmerCode.GetCode() ) ;
//printf( "%d %lld %lld\n", j, (long long int)kmerCode, (long long int)fixedKmerCode ) ;
if ( !kmers->IsIn( kmerCode ) )
continue ;
if ( minTo == tag + 1 )
minTo = i ;
++testCnt ;
// How many kmers this change can fix
for ( k = from ; k >= to ; --k )
{
kmerCode.Prepend( read[k] ) ;
if ( !kmers->IsIn( kmerCode ) )
break ;
}
// try extension
if ( k < to && to == 0 )
{
int l, m ;
for ( m = 0 ; m < kmerLength - 1 - ( from - to + 1 ) ; ++m )
{
for ( l = 0 ; l < 4 ; ++l )
{
KmerCode tmpKmerCode( kmerCode ) ;
tmpKmerCode.Prepend( numToNuc[l] ) ;
if ( kmers->IsIn( tmpKmerCode ) )
break ;
}
if ( l < 4 )
{
//printf( "hi\n" ) ;
kmerCode.Prepend( numToNuc[l] ) ;
--k ;
}
}
}
if ( k < minTo )
{
minCnt = 1 ;
minTo = k ;
minChange = j ;
tmpKmerCode = kmerCode ;
}
else if ( k == minTo )
{
++minCnt ;
if ( k == i - 1 && j == nucToNum[ read[i] - 'A' ] )
{
minCnt = 1 ;
minChange = j ;
tmpKmerCode = kmerCode ;
}
else if ( k == i -1 && minChange == nucToNum[ read[i] - 'A' ] )
{
minCnt = 1 ;
}
}
}
#ifdef DEBUG
printf( "-hi %d: %d %d=>%d, (%d)\n", i, minTo, to, minChange, minCnt ) ;
#endif
if ( testCnt > 1 )
alternativeCnt += ( testCnt - 1 ) ;
if ( minTo == readLength + 1 || ( minCnt > 1 && ( minTo >= to || i - to + 1 < kmerLength ) ) )
{
//printf( "-%s\n", read ) ;
//return -1 ;
if ( minTo == readLength + 1 )
noCandidateKmer = true ;
badPrefix = i + 1 ;
info = 2 ;
break ;
}
//printf( "---%d %d\n", minChange, nucToNum[read[0] - 'A'] ) ;
fix[i] = minChange ;
if ( minCnt > 1 )
{
fix[i] = -2 ;
++ambiguousCnt ;
}
if ( minTo < 0 )
break ;
if ( minTo >= to )
{
/*if ( maxTo > i + 1 )
{
// The next start search can start one place earlier
kmerCode = tmpKmerCode >> 2ull ;
i = maxTo - 1 ;
}
else*/
//kmerCode = tmpKmerCode << 2ull ;
kmerCode = tmpKmerCode ;
kmerCode.Append( 'A' ) ;
//printf( "i=>minTo: %d=>%d\n", i, minTo ) ;
i = minTo ;
continue ;
}
else
{
// Search for next error.
for ( k = to - 1 ; k >= 0 ; --k )
if ( !storedKmer[k] )
break ;
if ( k < 0 )
break ;
kmerCode.Restart() ;
for ( i = k + 2 - 1 ; i < k + 2 + kmerLength - 1 - 1 ; ++i )
{
if ( fix[i] < 0 )
kmerCode.Append( read[i] ) ;
else
kmerCode.Append( numToNuc[ fix[i] ] ) ;
}
i = k + 1 - 1 ;
kmerCode.Append( 'A' ) ;
continue ;
}
/*{
// This happens when the distance between two errors is just of kmerLength
//printf( "%llu\n", tmpKmerCode.GetCode() ) ;
kmerCode = tmpKmerCode ;
i = minTo ;
}*/
}
#ifdef DEBUG
printf( "fix: ") ;
for ( i = 0 ; i < readLength; ++i )
{
if ( fix[i] == -1 )
printf( "5" ) ;
else if ( fix[i] == -2 )
printf( "6" ) ;
else
printf( "%d", fix[i] ) ;
}
printf( "\n" ) ;
#endif
int ret = 0 ;
double correctCnt = 0 ;
//printf( "%s\n%d\n", read, ret ) ;
/*for ( i = badPrefix ; i < trimStart ; ++i )
{
if ( trusted[i] && fix[i] != -1 )
return -1 ;
if ( fix[i] == -1 || read[i] == numToNuc[ fix[i] ] || read[i] == 'N' )
continue ;
++correctCnt ;
if ( correctCnt > maxCorrection )
{
// There are too many corrections, adjust the trimStart
for ( j = i - 1 ; j >= badPrefix ; --j )
{
if ( fix[j] == -1 || read[j] == numToNuc[ fix[j] ] )
break ;
}
trimStart = j + 1 ;
if ( trimStart == badPrefix )
return -1 ;
correctCnt = 0 ;
for ( i = badPrefix ; i < trimStart ; ++i )
{
if ( fix[i] == -1 || read[i] == numToNuc[ fix[i] ] )
continue ;
++correctCnt ;
}
if ( correctCnt > maxCorrection - 1 )
return -1 ;
break ;
}
}*/
bool overCorrected = false ;
int adjustMaxCor = 0 ;
for ( i = 0 ; i < readLength ; ++i )
if ( trusted[i] && fix[i] != -1 )
break ;
if ( alternativeCnt == 0 && i >= readLength )
adjustMaxCor = 1 ;
for ( i = 0 ; i < readLength ; ++i )
{
int overCorrectWindow = 20 ;
if ( i >= overCorrectWindow && ( fix[i - overCorrectWindow] >= 0 && read[i - overCorrectWindow] != 'N' ) )
{
if ( qual[0] != '\0' && qual[i - overCorrectWindow] <= badQuality )
correctCnt -= 0.5 ;
else
--correctCnt ;
}
if ( fix[i] >= 0 && read[i] != 'N' )
{
if ( qual[0] != '\0' && qual[i] <= badQuality )
correctCnt += 0.5 ;
else
++correctCnt ;
}
int tmp = maxCorrection ;
if ( i >= overCorrectWindow && i + overCorrectWindow - 1 < readLength )
tmp += adjustMaxCor ;
if ( correctCnt > tmp ) //maxCorrection )
{
if ( fix[i] >= 0 )
{
fix[i] = 4 ;
overCorrected = true ;
}
}
}
if ( overCorrected )
{
for ( i = 0 ; i < readLength ; ++i )
{
if ( fix[i] == 4 )
{
fix[i] = -1 ;
int tag = i ;
for ( j = i - 1 ; j >= 0 && j >= tag - kmerLength + 1 ; --j )