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ErrorCorrection.cpp
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#include "ErrorCorrection.h"
#include <vector>
//#define DEBUG
#define MAX_TRIAL 1025
extern char nucToNum[26] ;
extern char numToNuc[26] ;
extern int MAX_FIX_PER_100 ;
extern int MAX_FIX_PER_K ;
extern double ERROR_RATE ;
extern bool VERBOSE ;
extern char badQualityThreshold ;
// Collect the information for fixing starting from a specific position
struct _fix
{
int fix[MAX_READ_LENGTH] ;
int bottleNeck ;
int fixCnt ;
} ;
struct _segmentInfo
{
int fixCnt ;
int bestFixCnt ;
int top2FixBottleNeck[2] ;
int lanchor, ranchor ;
int from, to ;
} ;
int CompInt( const void *p1, const void *p2 )
{
return *(int *)p1 - *(int *)p2 ;
}
void PrintKmer( KmerCode &kcode )
{
int kl = kcode.GetKmerLength() ;
int i ;
for ( i = kl - 1 ; i >= 0 ; --i )
{
printf( "%c", numToNuc[ ( kcode.GetCode() ) >> (uint64_t)( i * 2 ) & 3ull ] ) ;
}
printf( "\n" ) ;
}
bool IsPolyA( char *buffer, int length, int threshold = 2 )
{
int i ;
int cnt = 0 ;
for ( i = 0 ; i < length ; ++i )
if ( buffer[i] == 'A' )
++cnt ;
if ( cnt >= length - threshold )
return true ;
cnt = 0 ;
for ( i = 0 ; i < length ; ++i )
if ( buffer[i] == 'T' )
++cnt ;
if ( cnt >= length - threshold )
return true ;
return false ;
}
void *ErrorCorrection_Thread( void *arg )
{
int i, ind ;
int correction ;//, badPrefix, badSuffix ;
struct _ErrorCorrectionThreadArg *myArg = ( struct _ErrorCorrectionThreadArg *)arg ;
KmerCode kcode( myArg->kmerLength ) ;
int increment = 1 ;
if ( myArg->interleaved )
{
increment = 2 ;
}
while ( 1 )
{
pthread_mutex_lock( myArg->lock ) ;
ind = myArg->batchUsed ;
myArg->batchUsed += increment ;
pthread_mutex_unlock( myArg->lock ) ;
//printf( "%d %d\n", ind, myArg->batchSize ) ;
if ( ind >= myArg->batchSize )
break ;
//correction = ErrorCorrection_Wrapper( myArg->readBatch[ind].seq, kmerCode, myArg->kmers,
// badPrefix, badSuffix ) ;
int t = -1, t1 = -1, t2 = -1 ;
if ( myArg->readBatch2 != NULL || myArg->interleaved )
{
t1 = GetStrongTrustedThreshold( myArg->readBatch[ind].seq, myArg->readBatch[ind].qual, kcode, *myArg->kmers ) ;
if ( myArg->readBatch2 != NULL )
t2 = GetStrongTrustedThreshold( myArg->readBatch2[ind].seq, myArg->readBatch2[ind].qual, kcode, *myArg->kmers ) ;
else if ( myArg->interleaved )
t2 = GetStrongTrustedThreshold( myArg->readBatch[ind + 1].seq, myArg->readBatch[ind + 1].qual, kcode, *myArg->kmers ) ;
t = ( t1 < t2 ) ? t1 : t2 ;
}
correction = ErrorCorrection( myArg->readBatch[ind].id, myArg->readBatch[ind].seq, myArg->readBatch[ind].qual, t, kcode, *myArg->kmers ) ;
myArg->readBatch[ind].correction = correction ;
myArg->readBatch[ind].badPrefix = 0 ;
myArg->readBatch[ind].badSuffix = 0 ;
GetKmerInformation( myArg->readBatch[ind].seq, myArg->kmerLength, *myArg->kmers,
myArg->readBatch[ind].l, myArg->readBatch[ind].m, myArg->readBatch[ind].h ) ;
if ( myArg->readBatch2 != NULL )
{
correction = ErrorCorrection( myArg->readBatch2[ind].id, myArg->readBatch2[ind].seq, myArg->readBatch2[ind].qual, t, kcode, *myArg->kmers ) ;
myArg->readBatch2[ind].correction = correction ;
myArg->readBatch2[ind].badPrefix = 0 ;
myArg->readBatch2[ind].badSuffix = 0 ;
GetKmerInformation( myArg->readBatch2[ind].seq, myArg->kmerLength, *myArg->kmers,
myArg->readBatch2[ind].l, myArg->readBatch2[ind].m, myArg->readBatch2[ind].h ) ;
}
if ( myArg->interleaved )
{
correction = ErrorCorrection( myArg->readBatch[ind + 1].id, myArg->readBatch[ind + 1].seq, myArg->readBatch[ind + 1].qual, t, kcode, *myArg->kmers ) ;
myArg->readBatch[ind + 1].correction = correction ;
myArg->readBatch[ind + 1].badPrefix = 0 ;
myArg->readBatch[ind + 1].badSuffix = 0 ;
GetKmerInformation( myArg->readBatch[ind + 1].seq, myArg->kmerLength, *myArg->kmers,
myArg->readBatch[ind + 1].l, myArg->readBatch[ind + 1].m, myArg->readBatch[ind + 1].h ) ;
}
}
pthread_exit( NULL ) ;
}
inline double GetBound( int c )
{
return c * ERROR_RATE + 6.0 * sqrt( c * ERROR_RATE ) + 1 ;
}
int InferPosThreshold( KmerCode &kcode, Store &kmers, int direction, int upperBound ) // -1:left, 1:right
{
int i ;
int ret ;
KmerCode tmpKcode = kcode ;
int maxCnt = 0 ;
int tmp ;
for ( i = 0 ; i < 4 ; ++i )
{
tmpKcode = kcode ;
if ( direction == -1 )
tmpKcode.Prepend( numToNuc[i] ) ;
else
tmpKcode.Append( numToNuc[i] ) ;
tmp = kmers.GetCount( tmpKcode ) ;
if ( tmp > maxCnt )
maxCnt = tmp ;
}
ret = GetBound( maxCnt ) ;
if ( ret < 1 )
ret = 1 ;
//return ret ;
//tmp = GetBound( upperBound ) ;
if ( upperBound > ret || upperBound <= 0 )
return ret ;
else
return upperBound ;
}
bool TestExtend( int t, KmerCode kcode, int depth, int direction, Store &kmers )
{
int i ;
KmerCode tmpKcode( kcode ) ;
if ( depth <= 0 )
return true ;
for ( i = 0 ; i < 4 ; ++i )
{
tmpKcode = kcode ;
if ( direction == 1 )
tmpKcode.Append( numToNuc[i] ) ;
else
tmpKcode.Prepend( numToNuc[i] ) ;
#ifdef DEBUG
printf( "%s %d %d: %d\n", __func__, i, depth, kmers.GetCount( tmpKcode ) ) ;
#endif
if ( kmers.GetCount( tmpKcode ) < t )
continue ;
if ( TestExtend( t, tmpKcode, depth - 1 , direction, kmers ) )
return true ;
}
return false ;
}
// Return how many possible candidates
void SearchPaths_Right( int start, int to, int pos, int t, bool isPaired, char *seq, int fixCnt, int *fix, int fixBottleNeck,
int &maxFixCnt, int *bestFix, int &bestFixCnt, int &bestFixBottleNeck, int top2FixBottleNeck[], bool isStrongTrusted[], bool isPolyAKmer[],
KmerCode &kcode, Store &kmers, int &trialCnt )
{
int i, cnt, tmpBottleNeck ;
int extension = 0 ;
int kmerLength = kcode.GetKmerLength() ;
int threshold ;
// Give up fixing this read
if ( trialCnt > MAX_TRIAL )
{
if ( maxFixCnt > 2 )
{
--maxFixCnt ;
bestFixCnt = 0 ; // Remove the result before
bestFixBottleNeck = -1 ;
trialCnt = 0 ;
}
else
return ;
}
if ( fixCnt > maxFixCnt )
return ;
//if ( !isPaired && fixCnt == maxFixCnt && fixBottleNeck < bestFixBottleNeck )
// return ;
if ( pos >= to )
{
if ( seq[pos] == '\0' )
{
/*int teThreshold = ( t < fixBottleNeck ? t : fixBottleNeck ) ;
int tmp = teThreshold ;
teThreshold = teThreshold - 2 * sqrt( teThreshold ) ;
if ( teThreshold < tmp / 2 )
teThreshold = tmp / 2 ;
if ( teThreshold < 1 )
teThreshold = 1 ;*/
//if ( !TestExtend( 1, kcode, 1, 1, kmers ) )
// return ;
}
if ( fixBottleNeck < t )
++fixCnt ;
if ( fixCnt < maxFixCnt )
{
top2FixBottleNeck[0] = fixBottleNeck ;
top2FixBottleNeck[1] = -1 ;
}
else if ( fixCnt == maxFixCnt )
{
if ( fixBottleNeck > top2FixBottleNeck[0] )
{
top2FixBottleNeck[1] = top2FixBottleNeck[0] ;
top2FixBottleNeck[0] = fixBottleNeck ;
}
else if ( fixBottleNeck > top2FixBottleNeck[1] )
{
top2FixBottleNeck[1] = fixBottleNeck ;
}
}
//printf( "%d %d %d %d\n", fixCnt, fixBottleNeck, maxFixCnt, bestFixBottleNeck ) ;
if ( fixCnt < maxFixCnt
|| /*( !isPaired && fixCnt == maxFixCnt
&& (double)rand() / RAND_MAX <= (double)fixBottleNeck / ( fixBottleNeck + bestFixBottleNeck ) )
|| ( isPaired &&*/( fixCnt == maxFixCnt && fixBottleNeck > bestFixBottleNeck ) )
{
if ( fixCnt < maxFixCnt )
trialCnt = -( maxFixCnt - fixCnt + 1 ) * MAX_TRIAL ;
for ( i = start ; i < pos ; ++i )
bestFix[i] = fix[i] ;
maxFixCnt = fixCnt ;
//if ( fixCnt == maxFixCnt )
// bestFixBottleNeck = 0 ;
bestFixBottleNeck = fixBottleNeck ;
bestFixCnt = 1 ;
}
else if ( fixCnt == maxFixCnt && fixBottleNeck == bestFixBottleNeck )
{
bestFixCnt += 1 ;
}
return ;
}
threshold = InferPosThreshold( kcode, kmers, 1, t ) ;
KmerCode tmpKcode = kcode ;
/*for ( i = 0 ; seq[i] ; ++i )
printf( "%d ", fix[i] ) ;
printf( "\n" ) ;*/
if ( nucToNum[ seq[pos] - 'A' ] != -1 )
{
tmpKcode.Append( seq[pos] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
#ifdef DEBUG
printf( "right: %d %d %c=>%c (%d, %d)\n", fixCnt, pos, seq[pos], seq[pos], cnt, bestFixBottleNeck ) ;
//PrintKmer( tmpKcode ) ;
#endif
if ( cnt >= threshold )
{
fix[pos] = -1 ;
tmpBottleNeck = fixBottleNeck ;
if ( cnt < tmpBottleNeck )
tmpBottleNeck = cnt ;
++extension ;
SearchPaths_Right( start, to, pos + 1, t, isPaired, seq, fixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}
else if ( threshold == 1 && t <= 2 )
{
// See if it is accidentally below the threshold, by jumping
int j, k = 0 ;
for ( i = pos ; cnt < threshold && k < kmerLength ; ++k )
{
++i ;
if ( i >= to )
break ;
tmpKcode.Append( seq[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
//PrintKmer( tmpKcode ) ;
}
if ( k < kmerLength && i < to )
{
for ( j = pos ; j <= i ; ++j )
fix[j] = -1 ;
++extension ;
tmpBottleNeck = fixBottleNeck ;
//tmpKcode.Prepend( 'A' ) ;
SearchPaths_Right( start, to, i + 1, t, isPaired, seq, fixCnt + 1, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}
}
}
char c[5] = "ACGT" ;
if ( isStrongTrusted[pos] == false && !isPolyAKmer[ pos - kmerLength + 1 ] )
{
for ( i = 0 ; i < 4 ; ++i )
{
if ( c[i] == seq[pos] )
continue ;
tmpKcode = kcode ;
tmpKcode.Append( c[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
if ( cnt >= threshold )
{
int tmpFixCnt = fixCnt ;
fix[pos] = i ;
++trialCnt ;
++extension ;
#ifdef DEBUG
printf( "right: %d %d %c=>%c (%d, %d)\n", fixCnt, pos, seq[pos], c[i], cnt, bestFixBottleNeck ) ;
#endif
if ( nucToNum[ seq[pos] - 'A' ] != -1 )
++tmpFixCnt ;
tmpBottleNeck = fixBottleNeck ;
if ( cnt < tmpBottleNeck )
tmpBottleNeck = cnt ;
SearchPaths_Right( start, to, pos + 1, t, isPaired, seq, tmpFixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted,
isPolyAKmer, tmpKcode, kmers, trialCnt ) ;
}
}
}
/*else if ( isPolyAKmer[ pos - kmerLength + 1 ] )
{
// Jump through the PolyA region.
tmpKcode = kcode ;
int dest = pos + kmerLength - 1 ;
for ( i = pos ; seq[i] && i < dest ; ++i )
{
tmpKcode.Append( seq[i] ) ;
if ( nucToNum[ seq[i] - 'A' ] < 0 )
{
dest += kmerLength ;
}
}
SearchPaths_Right( start, dest + 1, t, seq, fixCnt, fix, fixBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}*/
// Jump through some unfixable region
if ( extension == 0 )
{
int j, k ;
tmpKcode = kcode ;
for ( i = pos ; i < to ; ++i )
{
threshold = InferPosThreshold( tmpKcode, kmers, 1, t ) ;
tmpKcode.Append( seq[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
fix[i] = -1 ;
if ( cnt >= threshold )
break ;
}
tmpBottleNeck = fixBottleNeck ;
/*tmpBottleNeck = 0 ;
for ( j = 0 ; j < 4 ; ++j )
{
KmerCode enumKmerCode = kcode ;
enumKmerCode.Append( numToNuc[j] ) ;
tmpBottleNeck += kmers.GetCount( enumKmerCode ) ;
}
if ( tmpBottleNeck > fixBottleNeck )
tmpBottleNeck = fixBottleNeck ;
else if ( tmpBottleNeck <= 0 )
tmpBottleNeck = 1 ;*/
if ( seq[i] )
{
k = i - pos - kmerLength + 1 ;
}
else
{
k = ( i - pos ) / 2 ;
//tmpBottleNeck = 0 ;
}
if ( k <= 0 )
k = 1 ;
#ifdef DEBUG
printf( "jump right: %d=>%d(%d)\n", pos, i, k ) ;
#endif
fixCnt += k ;
if ( i >= to )
i -= 1 ;
//tmpKcode.Prepend( 'A' ) ;
SearchPaths_Right( start, to, i + 1, t, isPaired, seq, fixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}
}
void SearchPaths_Left( int start, int to, int pos, int t, bool isPaired, char *seq, int fixCnt, int *fix, int fixBottleNeck,
int &maxFixCnt, int *bestFix, int &bestFixCnt, int &bestFixBottleNeck, int top2FixBottleNeck[], bool isStrongTrusted[], bool isPolyAKmer[],
KmerCode &kcode, Store &kmers, int &trialCnt )
{
int i, cnt, tmpBottleNeck ;
int extension = 0 ;
int kmerLength = kcode.GetKmerLength() ;
int threshold = t ;
if ( trialCnt > MAX_TRIAL )
{
if ( maxFixCnt > 2 )
{
--maxFixCnt ;
bestFixCnt = 0 ; // Remove the result before
bestFixBottleNeck = -1 ;
trialCnt = 0 ;
}
else
return ;
}
if ( fixCnt > maxFixCnt ) // TODO: it is possible that a wrong path has smaller fix point but with much lower bottleneck
return ;
if ( pos < to )
{
if ( pos <= -1 )
{
/*int teThreshold = ( t < fixBottleNeck ? t : fixBottleNeck ) ;
int tmp = teThreshold ;
teThreshold = teThreshold - 2 * sqrt( teThreshold ) ;
if ( teThreshold < tmp / 2 )
teThreshold = tmp / 2 ;
if ( teThreshold < 1 )
teThreshold = 1 ;*/
//if ( !TestExtend( 1, kcode, 3, -1, kmers ) )
// return ;
}
if ( fixBottleNeck < t )
++fixCnt ;
if ( fixCnt < maxFixCnt )
{
top2FixBottleNeck[0] = fixBottleNeck ;
top2FixBottleNeck[1] = -1 ;
}
else if ( fixCnt == maxFixCnt )
{
if ( fixBottleNeck > top2FixBottleNeck[0] )
{
top2FixBottleNeck[1] = top2FixBottleNeck[0] ;
top2FixBottleNeck[0] = fixBottleNeck ;
}
else if ( fixBottleNeck > top2FixBottleNeck[1] )
{
top2FixBottleNeck[1] = fixBottleNeck ;
}
}
//printf( "%d %d %d %d\n", fixCnt, fixBottleNeck, maxFixCnt, bestFixBottleNeck ) ;
if ( fixCnt < maxFixCnt
|| /*( !isPaired && fixCnt == maxFixCnt
&& (double)rand() / RAND_MAX <= (double)fixBottleNeck / ( fixBottleNeck + bestFixBottleNeck ) )
|| ( isPaired &&*/ ( fixCnt == maxFixCnt && fixBottleNeck > bestFixBottleNeck ) )
{
if ( fixCnt < maxFixCnt )
trialCnt = -( maxFixCnt - fixCnt + 1 ) * MAX_TRIAL ;
for ( i = start ; i > pos ; --i )
bestFix[i] = fix[i] ;
maxFixCnt = fixCnt ;
//if ( fixCnt == maxFixCnt )
// bestFixBottleNeck = 0 ;
bestFixBottleNeck = fixBottleNeck ;
bestFixCnt = 1 ;
}
else if ( fixCnt == maxFixCnt && fixBottleNeck == bestFixBottleNeck )
{
bestFixCnt += 1 ;
}
return ;
}
threshold = InferPosThreshold( kcode, kmers, -1, t ) ;
KmerCode tmpKcode = kcode ;
/*for ( i = 0 ; seq[i] ; ++i )
printf( "%d ", fix[i] ) ;
printf( "\n" ) ;*/
if ( nucToNum[ seq[pos] - 'A' ] != -1 )
{
tmpKcode.Prepend( seq[pos] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
#ifdef DEBUG
printf( "left: %d %d %c=>%c (%d[%d], %d)\n", fixCnt, pos, seq[pos], seq[pos], cnt, threshold, bestFixBottleNeck ) ;
#endif
if ( cnt >= threshold )
{
fix[pos] = -1 ;
tmpBottleNeck = fixBottleNeck ;
if ( cnt < tmpBottleNeck )
tmpBottleNeck = cnt ;
++extension ;
SearchPaths_Left( start, to, pos - 1, threshold, isPaired, seq, fixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}
else if ( threshold == 1 && t <= 2 )
{
// See if it is accidentally below the threshold
int j, k = 0 ;
for ( i = pos ; cnt < threshold && k < kmerLength ; ++k )
{
--i ;
if ( i < to )
break ;
tmpKcode.Prepend( seq[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
}
if ( k < kmerLength && i >= to )
{
for ( j = i ; j <= pos ; ++j )
fix[j] = -1 ;
tmpBottleNeck = fixBottleNeck ;
++extension ;
SearchPaths_Left( start, to, i - 1, threshold, isPaired, seq, fixCnt + 1, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted,
isPolyAKmer, tmpKcode, kmers, trialCnt ) ;
}
}
}
char c[5] = "ACGT" ;
if ( isStrongTrusted[pos] == false && !isPolyAKmer[pos] )
{
for ( i = 0 ; i < 4 ; ++i )
{
if ( c[i] == seq[pos] )
continue ;
tmpKcode = kcode ;
tmpKcode.Prepend( c[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
//printf( "%d: %c %d %lld %s\n", pos, c[i], cnt, tmpKcode.GetCode(), &seq[pos] ) ;
if ( cnt >= threshold )
{
int tmpFixCnt = fixCnt ;
fix[pos] = i ;
++trialCnt ;
#ifdef DEBUG
printf( "left: %d %d %c=>%c (%d[%d], %d)\n", fixCnt, pos, seq[pos], c[i], cnt, threshold, bestFixBottleNeck ) ;
#endif
if ( nucToNum[ seq[pos] - 'A' ] != -1 )
++tmpFixCnt ;
tmpBottleNeck = fixBottleNeck ;
if ( cnt < tmpBottleNeck )
tmpBottleNeck = cnt ;
++extension ;
SearchPaths_Left( start, to, pos - 1, threshold, isPaired, seq, tmpFixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck,
isStrongTrusted, isPolyAKmer, tmpKcode, kmers, trialCnt ) ;
}
}
}
/*else if ( isPolyAKmer[ pos] )
{
// Jump through the PolyA region.
tmpKcode = kcode ;
int dest = pos - kmerLength + 1 ;
for ( i = pos ; i >= 0 && i > dest ; --i )
{
tmpKcode.Prepend( seq[i] ) ;
if ( nucToNum[ seq[i] - 'A'] < 0 )
{
dest -= kmerLength ;
}
}
SearchPaths_Left( start, dest - 1, t, seq, fixCnt, fix, fixBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}*/
// Jump through some unfixable region
if ( extension == 0 )
{
int k ;
tmpKcode = kcode ;
for ( i = pos ; i >= to ; --i )
{
threshold = InferPosThreshold( tmpKcode, kmers, -1, t ) ;
tmpKcode.Prepend( seq[i] ) ;
cnt = kmers.GetCount( tmpKcode ) ;
fix[i] = -1 ;
if ( cnt >= threshold )
break ;
}
tmpBottleNeck = fixBottleNeck ;
/*tmpBottleNeck = 0 ;
int j ;
for ( j = 0 ; j < 4 ; ++j )
{
KmerCode enumKmerCode = kcode ;
enumKmerCode.Prepend( numToNuc[j] ) ;
tmpBottleNeck += kmers.GetCount( enumKmerCode ) ;
}
if ( tmpBottleNeck > fixBottleNeck )
tmpBottleNeck = fixBottleNeck ;
else if ( tmpBottleNeck <= 0 )
tmpBottleNeck = 1 ;*/
if ( i >= 0 )
{
k = pos - i - kmerLength + 1 ;
}
else
{
k = pos - 1 ;
//tmpBottleNeck = 0 ;
}
if ( k <= 0 )
k = 1 ;
#ifdef DEBUG
printf( "jump left: %d=>%d(%d)\n", pos, i, k ) ;
#endif
fixCnt += k ;
if ( i <= to )
++i ;
SearchPaths_Left( start, to, i - 1, threshold, isPaired, seq, fixCnt, fix, tmpBottleNeck,
maxFixCnt, bestFix, bestFixCnt, bestFixBottleNeck, top2FixBottleNeck, isStrongTrusted, isPolyAKmer, tmpKcode, kmers,
trialCnt ) ;
}
}
int ErrorCorrection( char *id, char *seq, char *qual, int pairStrongTrustThreshold, KmerCode &kcode, Store &kmers )
{
//printf( "Correct %s\n", seq ) ; fflush( stdout ) ;
if ( VERBOSE )
{
printf( "%s\n", id ) ;
}
int i, j, k ;
int kcnt = 0 ;
int kmerLength = kcode.GetKmerLength() ;
int readLength ;
int counts[MAX_READ_LENGTH] ;
int iBuffer[MAX_READ_LENGTH], fix[MAX_READ_LENGTH] ;
double dBuffer[MAX_READ_LENGTH] ;
bool isStrongTrusted[MAX_READ_LENGTH] ;
bool isPolyAKmer[MAX_READ_LENGTH] ;
int tstart, tend, longestTrustedLength, trustThreshold ;
//int searchResult ;
int totalFix= 0, allowedFix ;
int badSegmentCnt = 0 ;
int ret ;
int fixBottleNeck, bestFixBottleNeck ;
int strongTrustThreshold ;
bool unfixable, forceNextRound ;
bool isPaired ;
bool flag ;
struct _segmentInfo segmentInfo[MAX_READ_LENGTH], trustedIsland[MAX_READ_LENGTH] ;
int segmentInfoCnt = 0, trustedIslandCnt = 0 ;
kcode.Restart() ;
for ( i = 0 ; i < kmerLength - 1 ; ++i )
kcode.Append( seq[i] ) ;
for ( ; seq[i] ; ++i, ++kcnt )
{
kcode.Append( seq[i] ) ;
counts[kcnt] = kmers.GetCount( kcode ) ;
}
//printf( "\n",seq ) ;
readLength = i ;
allowedFix = readLength ;//* MAX_FIX_PER_100 / 100 ;
unfixable = false ;
isPaired = pairStrongTrustThreshold == -1 ? false : true ;
//isPaired = true ;
//printf( "%d\n", allowedFix ) ;
// Test whether there are too many Ns
k = 0 ;
for ( i = 0 ; i < readLength ; ++i )
if ( seq[i] == 'N' )
++k ;
if ( k > 5 )
return -1 ;
// Test whether there are too many A
k = 0 ;
for ( i = 0 ; i < readLength ; ++i )
if ( seq[i] == 'A' )
++k ;
if ( k > readLength - kmerLength )
return -1 ;
k = 0 ;
for ( i = 0 ; i < readLength ; ++i )
if ( seq[i] == 'T' )
++k ;
if ( k > readLength - kmerLength )
return -1 ;
//printf( "%s\n", seq ) ;
if ( VERBOSE )
{
printf( "Before correction:\n%s\n", seq ) ;
for ( i = 0 ; i < kcnt ; ++i )
{
if ( counts[i] != 0 )
printf( "%d ", counts[i] ) ;
else
printf( "1 " ) ;
}
printf( "\n" ) ;
}
trustThreshold = 2 ;
for ( i = 0 ; i < kcnt ; ++i )
{
int t = 7 ;
if ( kmerLength / 2 > t )
t = kmerLength / 2 ;
if ( IsPolyA( seq + i, kmerLength, t ) )
iBuffer[i] = -1 ;
else
iBuffer[i] = counts[i] ;
}
qsort( iBuffer, kcnt, sizeof( int ), CompInt ) ;
for ( i = kcnt - 1 ; i >= 1 ; --i )
{
if ( iBuffer[i] > 2 * iBuffer[i - 1] && iBuffer[i] > 10 )
break ;
}
flag = false ;
if ( i >= 1 )
//if ( i < kcnt )
{
//trustThreshold = iBuffer[( kcnt - 1 + i ) / 2] / 20 + 1 ;
trustThreshold = GetBound( iBuffer[i] ) ;
strongTrustThreshold = iBuffer[i] ;
if ( strongTrustThreshold >= 20 && iBuffer[i - 1] == 2 && trustThreshold < 3 )
{
flag = true ;
trustThreshold = 3 ;
}
//trustThreshold = iBuffer[kcnt / 2] - 4 * sqrt( iBuffer[i] ) ;
}
else
{
//trustThreshold = iBuffer[kcnt / 2] - 4 * sqrt( iBuffer[kcnt / 2 ] ) ;
for ( i = 0 ; i < kcnt ; ++i )
if ( iBuffer[i] > 0 )
break ;
strongTrustThreshold = iBuffer[ ( i + kcnt - 1 ) / 2 ] ;
trustThreshold = GetBound( strongTrustThreshold ) ;
}
if ( pairStrongTrustThreshold >= 1 && strongTrustThreshold > pairStrongTrustThreshold )
{
if ( flag == false || pairStrongTrustThreshold < 20 )
trustThreshold = GetBound( pairStrongTrustThreshold ) ;
strongTrustThreshold = pairStrongTrustThreshold ;
}
for ( i = 0 ; i < kcnt ; ++i )
{
if ( IsPolyA( seq + i, kmerLength ) )
isPolyAKmer[i] = true ;
else
isPolyAKmer[i] = false ;
}
/*#ifdef DEBUG
printf( "isPolyAKmer:\n") ;
for ( i = 0 ; i < kcnt ; ++i )
{
printf( "%d", isPolyAKmer[i] ) ;
}
printf( "\n" ) ;
#endif*/
//trustThreshold /= 2 ;
if ( trustThreshold < 2 )
trustThreshold = 2 ;
//if ( trustThreshold > 10 )
// trustThreshold = 10 ;
//if ( trustThreshold >= 10 )
// allowedFix -= trustThreshold / 10 ;
//if ( allowedFix < 0 )
// allowedFix = 0 ;
// Try different thresholds
int iter = 0 ;
while ( 1 )
{
if ( VERBOSE )
printf( "strong trust threshold=%d threshold=%d\n", strongTrustThreshold, trustThreshold ) ;
allowedFix = readLength ;//* MAX_FIX_PER_100 / 100 ;
totalFix = 0 ;
unfixable = false ;
forceNextRound = false ;
// Find the longest trusted portion
trustedIslandCnt = 0 ;
longestTrustedLength = -1 ;
j = 0 ;
memset( isStrongTrusted, false, sizeof( bool ) * readLength ) ;
for ( i = 0 ; i < readLength ; ++i )
iBuffer[i] = -1 ;
for ( i = 0 ; i < kcnt ; ++i )
{
//int t = 7 ;
//if ( kmerLength / 2 > t )
// t = kmerLength / 2 ;
if ( counts[i] >= strongTrustThreshold && !IsPolyA( seq + i, kmerLength ) )
{
//printf( "(%d %d)\n", counts[i], strongTrustThreshold ) ;
++j ;
}
else
{
if ( j > longestTrustedLength )
{
longestTrustedLength = j ;
tstart = i - longestTrustedLength ;
tend = i - 1 ;
}
if ( j >= 2 )
{
//printf( "%d %d: %d %d\n", i, j, i - j, i - 1 + kmerLength - 1 ) ;
/*for ( k = i - j ; k <= i - 1 + kmerLength - 1 ; ++k )
{
if ( iBuffer[k] == -1 )
isStrongTrusted[k] = true ;
else
isStrongTrusted[k] = false ;
//iBuffer[k] = i - j ;
}*/
trustedIsland[ trustedIslandCnt ].from = i - j ;
trustedIsland[ trustedIslandCnt ].to = i - 1 ;
++trustedIslandCnt ;
}
/*if ( IsPolyA( seq + i, kmerLength ) )
{
for ( k = i ; k < i + kmerLength ; ++i )
isStrongTrusted[k] = true ;
}*/
j = 0 ;
}
}
if ( j > longestTrustedLength )
{
longestTrustedLength = j ;
tstart = i - longestTrustedLength ;
tend = i - 1 ;
}
if ( j >= 2 )
{
/*for ( k = i - j ; k <= i - 1 + kmerLength - 1 ; ++k )
{
if ( iBuffer[k] == -1 )
isStrongTrusted[k] = true ;
else
isStrongTrusted[k] = false ;
//iBuffer[k] = i - j ;
}*/
trustedIsland[ trustedIslandCnt ].from = i - j ;
trustedIsland[ trustedIslandCnt ].to = i - 1 ;
++trustedIslandCnt ;
}
// Adjust the boundary of trusted kmer islands
for ( i = 1 ; i < trustedIslandCnt ; ++i )
{
if ( trustedIsland[i].from <= trustedIsland[i - 1].to + kmerLength - 1 + 1 )
{
int len1 = trustedIsland[i - 1].to - trustedIsland[i - 1].from ;
int len2 = trustedIsland[i].to - trustedIsland[i].from ;
int overlap = trustedIsland[i - 1].to + kmerLength - 1 + 1 - trustedIsland[i].from ;
//printf( "%d\n", overlap ) ;
// check the count between them
for ( j = trustedIsland[i - 1].to + 1 ; j < trustedIsland[i].from ; ++j )
{
if ( counts[j] <= 2 && counts[j] < trustThreshold )
break ;
}
if ( j >= trustedIsland[i].from )
continue ;
if ( overlap > 3 )
continue ;
if ( len1 < len2 )
{
// change the i-1 island
trustedIsland[i - 1].to -= ( overlap + 1 ) ;
}
else
{
trustedIsland[i].from += ( overlap + 1 ) ;
}
}
}
// Set trusted positions
for ( i = 0 ; i < trustedIslandCnt ; ++i )
{
if ( trustedIsland[i].from > trustedIsland[i].to )
continue ;
for ( j = trustedIsland[i].from ; j <= trustedIsland[i].to + kmerLength - 1 ; ++j )
isStrongTrusted[j] = true ;
}
trustedIslandCnt = 0 ;
j = -1 ;
for ( i = 0 ; seq[i] ; ++i )
{
if ( j == -1 && isStrongTrusted[i] == true )
{
j = i ;
}
if ( j != -1 && isStrongTrusted[i] == false && isStrongTrusted[i - 1] == true )
{
trustedIsland[ trustedIslandCnt ].from = j ;
trustedIsland[ trustedIslandCnt ].to = i - 1 ;
++trustedIslandCnt ;
j = -1 ;
}
}
if ( j != -1 )
{
trustedIsland[ trustedIslandCnt ].from = j ;
trustedIsland[ trustedIslandCnt ].to = i - 1 ;
++trustedIslandCnt ;
j = -1 ;
}
if ( trustedIslandCnt == 0 )
{