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orderContig.c
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orderContig.c
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#include "stdinc.h"
#include "newhash.h"
#include "kmerhash.h"
#include "extfunc.h"
#include "extvab.h"
#include "dfibHeap.h"
#include "fibHeap.h"
#include "darray.h"
#include "zlib.h"
#define CNBLOCKSIZE 10000
#define MAXC 10000
#define MAXCinBetween 200
#define MaxNodeInSub 10000
#define GapLowerBound -2000
#define GapUpperBound 300000
#define MaxCntNode 1000
/*
static int DEBUG = 0;
static int DEBUG1 = 0;
static int DEBUG2 = 0;
*/
static int bySmall = 1;
static boolean static_f = 0;
static double OverlapPercent = 0.05;
static double ConflPercent = 0.05;
static int MinWeakCut = 3;
static int gapCounter;
static int orienCounter;
static int orienCounter2;
static int throughCounter;
static int breakPointAtRepeat = 0;
static FILE *snp_fp = NULL;
static DARRAY *solidArray;
static DARRAY *tempArray;
static int solidCounter;
static CTGinHEAP ctg4heapArray[MaxNodeInSub + 1];
static unsigned int nodesInSub[MaxNodeInSub];
static int nodeDistance[MaxNodeInSub];
static int nodeCounter;
static int dCntCounter1;
static int uCntCounter1;
static int dCntCounter2;
static int uCntCounter2;
static unsigned int dCntNodeArr1[MaxCntNode]; //downstream
static unsigned int uCntNodeArr1[MaxCntNode]; //upstream
static int dCntGapArr1[MaxCntNode];
static int uCntGapArr1[MaxCntNode];
static unsigned int dCntNodeArr2[MaxCntNode];
static unsigned int uCntNodeArr2[MaxCntNode];
static int dCntGapArr2[MaxCntNode];
static int uCntGapArr2[MaxCntNode];
static unsigned int *cntNodeArr;
static int *cntGapArr;
static unsigned int nodesInSubInOrder[MaxNodeInSub];
static int nodeDistanceInOrder[MaxNodeInSub];
static DARRAY *scaf3, *scaf5;
static DARRAY *gap3, *gap5;
static unsigned int downstreamCTG[MAXCinBetween];
static unsigned int upstreamCTG[MAXCinBetween];
static int dsCtgCounter;
static int usCtgCounter;
static CONNECT *checkConnect ( unsigned int from_c, unsigned int to_c );
static int maskPuzzle ( int num_connect, unsigned int contigLen );
static void freezing();
static boolean checkOverlapInBetween ( double tolerance );
static int setConnectDelete ( unsigned int from_c, unsigned int to_c, char flag, boolean cleanBinding );
static int setConnectMask ( unsigned int from_c, unsigned int to_c, char mask );
static int setConnectWP ( unsigned int from_c, unsigned int to_c, char flag );
static void general_linearization ( boolean strict );
static void debugging2();
static void smallScaf();
static void clearNewInsFlag();
static void detectBreakScaff();
static void detectBreakScaf();
static boolean checkSimple ( DARRAY *ctgArray, int count );
static void checkCircle();
/*************************************************
Function:
checkFiles4Scaff
Description:
Checks the required files for scaffolding.
Input:
1. infile: prefix of graph
Output:
None.
Return:
1 if all files were OK.
*************************************************/
boolean checkFiles4Scaff ( char *infile )
{
char name[7][256];
boolean filesOK = 1;
int i = 0;
sprintf ( name[0], "%s.Arc", infile );
sprintf ( name[1], "%s.contig", infile );
sprintf ( name[2], "%s.peGrads", infile );
sprintf ( name[3], "%s.preGraphBasic", infile );
sprintf ( name[4], "%s.updated.edge", infile );
sprintf ( name[5], "%s.readOnContig.gz", infile );
for ( ; i < 6; i++ )
{
filesOK = check_file ( name[i] );
if ( !filesOK )
{
fprintf ( stderr, "%s: no such file or empty file!\n\n", name[i] );
return filesOK;
}
}
fprintf ( stderr, "Files for scaffold construction are OK.\n\n" );
return filesOK;
}
/*************************************************
Function:
getBindCnt
Description:
Gets the only connection of current contig.
Input:
1. ctg: current contig
Output:
None.
Return:
The pointer to connection if only one connection was found.
*************************************************/
static CONNECT *getBindCnt ( unsigned int ctg )
{
CONNECT *ite_cnt;
CONNECT *bindCnt = NULL;
CONNECT *temp_cnt = NULL;
CONNECT *temp3_cnt = NULL;
int count = 0;
int count2 = 0;
int count3 = 0;
ite_cnt = contig_array[ctg].downwardConnect;
while ( ite_cnt )
{
if ( ite_cnt->nextInScaf )
{
count++;
bindCnt = ite_cnt;
}
if ( ite_cnt->prevInScaf )
{
temp_cnt = ite_cnt;
count2++;
}
if ( ite_cnt->singleInScaf )
{
temp3_cnt = ite_cnt;
count3++;
}
ite_cnt = ite_cnt->next;
}
if ( count == 1 )
{
return bindCnt;
}
if ( count == 0 && count2 == 1 )
{
return temp_cnt;
}
if ( count == 0 && count2 == 0 && count3 == 1 )
{
return temp3_cnt;
}
return NULL;
}
/*************************************************
Function:
createAnalogousCnt
Description:
Creats new relation between two non-connected contigs
according to toplogy sturcture supported by large insert size
paired-end reads.
Input:
1. sourceStart: contig that has connection relations to other two
contigs
2. originCnt: direct connection supported by large insert size
paired-end reads
3. gap: calculated distance between two non-connected contigs
4. targetStart: left contig of those two non-connected contigs
5. targetStop: right contig of those two non-connected contigs
Output:
None.
Return:
1 if creation successed.
*************************************************/
static boolean createAnalogousCnt ( unsigned int sourceStart,
CONNECT *originCnt, int gap,
unsigned int targetStart, unsigned int targetStop )
{
CONNECT *temp_cnt;
unsigned int balTargetStart = getTwinCtg ( targetStart );
unsigned int balTargetStop = getTwinCtg ( targetStop );
unsigned int balSourceStart = getTwinCtg ( sourceStart );
unsigned int balSourceStop = getTwinCtg ( originCnt->contigID );
boolean change_flag = 0;
int add_weight = originCnt->weight;
if ( gap < GapLowerBound )
{
gapCounter++;
originCnt->deleted = 1;
temp_cnt = getCntBetween ( balSourceStop, balSourceStart );
temp_cnt->deleted = 1;
return change_flag;
}
int startLen = ( int ) contig_array[targetStart].length;
int stopLen = ( int ) contig_array[targetStop].length;
if ( gap < -overlaplen )
{
if ( ( int ) contig_array[targetStart].length - overlaplen <= -gap && ( int ) contig_array[targetStart].length > 5 * overlaplen )
{
unsigned int tmp_id = targetStart;
targetStart = targetStop;
targetStop = tmp_id;
tmp_id = balTargetStart;
balTargetStart = balTargetStop;
balTargetStop = tmp_id;
gap = -gap;
change_flag = 1;
}
else
{
gapCounter++;
return change_flag;
}
}
originCnt->deleted = 1;
temp_cnt = getCntBetween ( balSourceStop, balSourceStart );
temp_cnt->deleted = 1;
temp_cnt = add1Connect ( targetStart, targetStop, gap, add_weight, 1 );
if ( temp_cnt )
{
temp_cnt->inherit = 1;
}
temp_cnt = add1Connect ( balTargetStop, balTargetStart, gap, add_weight, 1 );
if ( temp_cnt )
{
temp_cnt->inherit = 1;
}
return change_flag;
}
/*************************************************
Function:
add1LongPEcov
Description:
Increases the connections weight supported by large insert size
paired-end reads between contigs in one scaffold.
Input:
1. fromCtg: left contig of pair contig connected by large insert
size paired-end reads
2. toCtg: right contig of pair contig connected by large insert
size paired-end reads
3. weight: weight of connection
Output:
None.
Return:
None.
*************************************************/
static void add1LongPEcov ( unsigned int fromCtg, unsigned int toCtg, int weight )
{
//check if they are on the same scaff
if ( contig_array[fromCtg].from_vt != contig_array[toCtg].from_vt ||
contig_array[fromCtg].to_vt != contig_array[toCtg].to_vt )
{
fprintf ( stderr, "Warning from add1LongPEcov: contig %d and %d not on the same scaffold\n",
fromCtg, toCtg );
return;
}
if ( contig_array[fromCtg].indexInScaf >= contig_array[toCtg].indexInScaf )
{
fprintf ( stderr, "Warning from add1LongPEcov: wrong about order between contig %d and %d\n",
fromCtg, toCtg );
return;
}
CONNECT *bindCnt;
unsigned int prevCtg = fromCtg;
bindCnt = getBindCnt ( fromCtg );
while ( bindCnt )
{
if ( bindCnt->maxGap + weight <= 1000 )
{
bindCnt->maxGap += weight;
}
else
{
bindCnt->maxGap = 1000;
}
if ( fromCtg == 0 && toCtg == 0 )
fprintf ( stderr, "link (%d %d ) covered by link (%d %d), wt %d\n",
prevCtg, bindCnt->contigID, fromCtg, toCtg, weight );
if ( bindCnt->contigID == toCtg )
{
break;
}
prevCtg = bindCnt->contigID;
bindCnt = bindCnt->nextInScaf;
}
unsigned int bal_fc = getTwinCtg ( fromCtg );
unsigned int bal_tc = getTwinCtg ( toCtg );
bindCnt = getBindCnt ( bal_tc );
prevCtg = bal_tc;
while ( bindCnt )
{
if ( bindCnt->maxGap + weight <= 1000 )
{
bindCnt->maxGap += weight;
}
else
{
bindCnt->maxGap = 1000;
}
if ( fromCtg == 0 && toCtg == 0 )
fprintf ( stderr, "link (%d %d ) covered by link (%d %d), wt %d\n",
prevCtg, bindCnt->contigID, fromCtg, toCtg, weight );
if ( bindCnt->contigID == bal_fc )
{
return;
}
prevCtg = bindCnt->contigID;
bindCnt = bindCnt->nextInScaf;
}
}
/*************************************************
Function:
downSlide
Description:
Deals with connections supported by large insert size paired-end
reads. If a connecton is abnormal, or the two connected contigs
are in the same scaffold and the distance between them is normal,
set the connection's status to 'deleted'. If the two connected
contigs locate in different scaffolds, trys to creat a connection
between these two scaffolds.
Input:
None.
Output:
None.
Return:
None.
*************************************************/
static void downSlide()
{
int len = 0, gap;
unsigned int i;
CONNECT *ite_cnt, *bindCnt, *temp_cnt;
unsigned int bottomCtg, topCtg, bal_i;
unsigned int targetCtg, bal_target;
boolean getThrough, orienConflict;
int slideLen, slideLen2;
int slideexchange1 = 0, slideexchange2 = 0;
orienCounter = throughCounter = 0;
orienCounter2 = 0;
int slidebreak1 = 0, slidebreak2 = 0, slidebreak = 0, recoverCnt = 0;
for ( i = 1; i <= num_ctg; i++ )
{
if ( contig_array[i].mask || !contig_array[i].downwardConnect )
{
continue;
}
bindCnt = getBindCnt ( i );
if ( !bindCnt )
{
continue;
}
bal_i = getTwinCtg ( i );
len = slideLen = 0;
bottomCtg = i;
//find the last unmasked contig in this binding
while ( bindCnt->nextInScaf )
{
len += bindCnt->gapLen + contig_array[bindCnt->contigID].length;
if ( contig_array[bindCnt->contigID].mask == 0 )
{
bottomCtg = bindCnt->contigID;
slideLen = len;
}
bindCnt = bindCnt->nextInScaf;
}
len += bindCnt->gapLen + contig_array[bindCnt->contigID].length;
if ( contig_array[bindCnt->contigID].mask == 0 || bottomCtg == 0 )
{
bottomCtg = bindCnt->contigID;
slideLen = len;
}
//check each connetion from long pair ends
ite_cnt = contig_array[i].downwardConnect;
while ( ite_cnt )
{
if ( ite_cnt->deleted || ite_cnt->mask || ite_cnt->singleInScaf
|| ite_cnt->nextInScaf || ite_cnt->prevInScaf || ite_cnt->inherit )
{
ite_cnt = ite_cnt->next;
continue;
}
targetCtg = ite_cnt->contigID;
if ( contig_array[i].from_vt == contig_array[targetCtg].from_vt ) // on the same scaff
{
if ( contig_array[i].indexInScaf > contig_array[targetCtg].indexInScaf )
{
orienCounter++;
}
else
{
throughCounter++;
}
setConnectDelete ( i, ite_cnt->contigID, 1, 0 );
ite_cnt = ite_cnt->next;
continue;
}
if ( ( ins_var_idx > 0 ) && ( slideLen > Insert_size * ins_var_idx ) )
{
setConnectDelete ( i, ite_cnt->contigID, 1, 0 );
ite_cnt = ite_cnt->next;
slidebreak1++;
continue;
}
//contig i and targetctg is not in same scaffold
//check if this connection conflicts with previous scaffold orientationally
temp_cnt = getBindCnt ( targetCtg );
orienConflict = 0;
if ( temp_cnt )
{
while ( temp_cnt->nextInScaf )
{
if ( temp_cnt->contigID == i )
{
orienConflict = 1;
fprintf ( stderr, "Warning from downSlide: still on the same scaff: %d and %d\n"
, i, targetCtg );
fprintf ( stderr, "on scaff %d and %d\n",
contig_array[i].from_vt, contig_array[targetCtg].from_vt );
fprintf ( stderr, "on bal_scaff %d and %d\n",
contig_array[bal_target].to_vt, contig_array[bal_i].to_vt );
break;
}
temp_cnt = temp_cnt->nextInScaf;
}
if ( temp_cnt->contigID == i )
{
orienConflict = 1;
}
}
if ( orienConflict )
{
orienCounter++;
orienCounter2++;
setConnectDelete ( i, ite_cnt->contigID, 1, 0 );
ite_cnt = ite_cnt->next;
continue;
}
//connection path to i was not found
//find the most top contig along previous scaffold starting with the target contig of this connection
bal_target = getTwinCtg ( targetCtg );
slideLen2 = 0;
if ( contig_array[targetCtg].mask == 0 )
{
topCtg = bal_target;
}
else
{
topCtg = 0;
}
temp_cnt = getBindCnt ( bal_target );
getThrough = len = 0;
int slidebreak = 0;
if ( temp_cnt )
{
//find the last contig in this binding
while ( temp_cnt->nextInScaf )
{
//check if this route reaches bal_i
if ( temp_cnt->contigID == bal_i )
{
fprintf ( stderr, "Warning from downSlide: (B) still on the same scaff: %d and %d (%d and %d)\n",
i, targetCtg, bal_target, bal_i );
fprintf ( stderr, "on scaff %d and %d\n",
contig_array[i].from_vt, contig_array[targetCtg].from_vt );
fprintf ( stderr, "on bal_scaff %d and %d\n",
contig_array[bal_target].to_vt, contig_array[bal_i].to_vt );
getThrough = 1;
break;
}
len += temp_cnt->gapLen + contig_array[temp_cnt->contigID].length;
if ( contig_array[temp_cnt->contigID].mask == 0 )
{
topCtg = temp_cnt->contigID;
slideLen2 = len;
}
if ( ( ins_var_idx > 0 ) && ( len > ins_var_idx * Insert_size ) )
{
slidebreak = 1;
break;
}
temp_cnt = temp_cnt->nextInScaf;
}
len += temp_cnt->gapLen + contig_array[temp_cnt->contigID].length;
if ( contig_array[temp_cnt->contigID].mask == 0 || topCtg == 0 )
{
topCtg = temp_cnt->contigID;
slideLen2 = len;
}
if ( slidebreak == 1 )
{
setConnectDelete ( i, ite_cnt->contigID, 1, 0 );
ite_cnt = ite_cnt->next;
slidebreak2++;
continue;
}
if ( temp_cnt->contigID == bal_i )
{
getThrough = 1;
}
else
{
topCtg = getTwinCtg ( topCtg );
}
}
else
{
topCtg = targetCtg;
}
if ( getThrough )
{
throughCounter++;
setConnectDelete ( i, ite_cnt->contigID, 1, 0 );
ite_cnt = ite_cnt->next;
continue;
}
//connection path to bal_id was not found
CONNECT *dh_cnt;
gap = ite_cnt->gapLen - slideLen - slideLen2;
dh_cnt = getCntBetween ( topCtg, bottomCtg );
if ( dh_cnt && dh_cnt->weight >= MinWeakCut )
{
slideexchange1++;
setConnectDelete ( topCtg, bottomCtg, 0, 0 );
setConnectMask ( topCtg, bottomCtg, 0 );
ite_cnt = ite_cnt->next;
continue;
}
//add a connection between bottomCtg and topCtg
if ( bottomCtg != topCtg && ! ( i == bottomCtg && targetCtg == topCtg ) )
{
boolean creat_flag = createAnalogousCnt ( i, ite_cnt, gap, bottomCtg, topCtg );
if ( creat_flag )
{
slideexchange2++;
}
if ( contig_array[bottomCtg].mask || contig_array[topCtg].mask )
{
fprintf ( stderr, "downSlide to masked contig, bottomCtg %u[mask %d], topCtg %u[mask %d]\n", bottomCtg, contig_array[bottomCtg].mask, topCtg, contig_array[topCtg].mask );
}
}
ite_cnt = ite_cnt->next;
}
}
// fprintf(stderr,"downSliding stat:\norienConflict\tfall_inside\tslidebreak1\tslidebreak2\trecoverCnt\tslideexchange1\tslideexchange2\n%d\t%d\t%d\t%d\t%d\t%d\t%d\n",orienCounter, throughCounter, slidebreak1, slidebreak2, recoverCnt, slideexchange1, slideexchange2);
fprintf ( stderr, "Add large insert size PE links: %d orientation-conflict links, %d contigs acrossed by normal links.\n", orienCounter, throughCounter );
}
/*************************************************
Function:
setNextInScaf
Description:
Sets the downstream connection of current connection.
Input:
1. cnt: current connection
2. nextCnt: next connection
Output:
None.
Return:
1 if setting successed.
*************************************************/
static boolean setNextInScaf ( CONNECT *cnt, CONNECT *nextCnt )
{
if ( !cnt )
{
fprintf ( stderr, "setNextInScaf: empty pointer\n" );
return 0;
}
if ( !nextCnt )
{
cnt->nextInScaf = nextCnt;
return 1;
}
if ( cnt->mask || cnt->deleted )
{
fprintf ( stderr, "setNextInScaf: cnt is masked or deleted\n" );
return 0;
}
if ( nextCnt->deleted || nextCnt->mask )
{
fprintf ( stderr, "setNextInScaf: nextCnt is masked or deleted\n" );
return 0;
}
cnt->nextInScaf = nextCnt;
return 1;
}
/*************************************************
Function:
setPrevInScaf
Description:
Sets the upstream connection status of current connection.
Input:
1. cnt: current connection
2. flag: new status
Output:
None.
Return:
1 if setting successed.
*************************************************/
static boolean setPrevInScaf ( CONNECT *cnt, boolean flag )
{
if ( !cnt )
{
fprintf ( stderr, "setPrevInScaf: empty pointer\n" );
return 0;
}
if ( !flag )
{
cnt->prevInScaf = flag;
return 1;
}
if ( cnt->mask || cnt->deleted )
{
fprintf ( stderr, "setPrevInScaf: cnt is masked or deleted\n" );
return 0;
}
cnt->prevInScaf = flag;
return 1;
}
/*************************************************
Function:
substitueUSinScaf
Description:
Substitutes the upstream connection of current connection with
new connection.
from_c
-> branch_c -> to_c
from_c_new
Input:
1. origin: original upstream connection of current connection
(from_c -> branch_c)
2. from_c_new: new upstream contig of current contig (branch_c)
Output:
None.
Return:
None.
*************************************************/
static void substitueUSinScaf ( CONNECT *origin, unsigned int from_c_new )
{
if ( !origin || !origin->nextInScaf )
{
return;
}
unsigned int branch_c, to_c;
unsigned int bal_branch_c, bal_to_c;
unsigned int bal_from_c_new = getTwinCtg ( from_c_new );
CONNECT *bal_origin, *bal_nextCNT, *prevCNT, *bal_prevCNT;
branch_c = origin->contigID;
to_c = origin->nextInScaf->contigID;
bal_branch_c = getTwinCtg ( branch_c );
bal_to_c = getTwinCtg ( to_c );
prevCNT = checkConnect ( from_c_new, branch_c );
bal_nextCNT = checkConnect ( bal_to_c, bal_branch_c );
if ( !bal_nextCNT )
{
fprintf ( stderr, "substitueUSinScaf: no connect between %d and %d\n", bal_to_c, bal_branch_c );
return;
}
bal_origin = bal_nextCNT->nextInScaf;
bal_prevCNT = checkConnect ( bal_branch_c, bal_from_c_new );
setPrevInScaf ( bal_nextCNT->nextInScaf, 0 );
setNextInScaf ( prevCNT, origin->nextInScaf );
setNextInScaf ( bal_nextCNT, bal_prevCNT );
setPrevInScaf ( bal_prevCNT, 1 );
setNextInScaf ( origin, NULL );
setPrevInScaf ( bal_origin, 0 );
}
/*************************************************
Function:
substitueDSinScaf
Description:
Substitutes the downstream connection of current connection with
new connection.
to_c
from_c -> branch_c ->
to_c_new
Input:
1. origin: original downstream connection of current connection
(branch_c -> to_c)
2. branch_c: current contig
3. to_c_new: new downstream contig of current contig
Output:
None.
Return:
None.
*************************************************/
static void substitueDSinScaf ( CONNECT *origin, unsigned int branch_c, unsigned int to_c_new )
{
if ( !origin || !origin->prevInScaf )
{
return;
}
unsigned int to_c;
unsigned int bal_branch_c, bal_to_c, bal_to_c_new;
unsigned int from_c, bal_from_c;
CONNECT *bal_origin, *prevCNT, *bal_prevCNT;
CONNECT *nextCNT, *bal_nextCNT;
to_c = origin->contigID;
bal_branch_c = getTwinCtg ( branch_c );
bal_to_c = getTwinCtg ( to_c );
bal_origin = getCntBetween ( bal_to_c, bal_branch_c );
if ( !bal_origin )
{
fprintf ( stderr, "substitueDSinScaf: no connect between %d and %d\n", bal_to_c, bal_branch_c );
return;
}
if ( bal_origin->nextInScaf )
{
bal_from_c = bal_origin->nextInScaf->contigID;
}
else
{
fprintf ( stderr, "next null! %d\t%d\n", bal_to_c, bal_branch_c );
exit ( 3 );
}
bal_from_c = bal_origin->nextInScaf->contigID;
from_c = getTwinCtg ( bal_from_c );
bal_to_c_new = getTwinCtg ( to_c_new );
prevCNT = checkConnect ( from_c, branch_c );
nextCNT = checkConnect ( branch_c, to_c_new );
setNextInScaf ( prevCNT, nextCNT );
setPrevInScaf ( nextCNT, 1 );
bal_nextCNT = checkConnect ( bal_to_c_new, bal_branch_c );
bal_prevCNT = checkConnect ( bal_branch_c, bal_from_c );
setNextInScaf ( bal_nextCNT, bal_prevCNT );
setPrevInScaf ( origin, 0 );
setNextInScaf ( bal_origin, NULL );
}
/*************************************************
Function:
validConnect
Description:
Calculates the valid connections number of a contig.
1. Check whether the contig has upstream conntcion and
downstream connection.
2. Calculates the non-deleted and non-masked connections number.
Input:
1. ctg: contig
2. preCNT: upstream connection
Output:
None.
Return:
0 if contig did NOT have connection to other contigs.
1 if contig had upstream conntcion and downstream connection.
Non-deleted and non-masked connections number otherwise.
*************************************************/
static int validConnect ( unsigned int ctg, CONNECT *preCNT )
{
if ( preCNT && preCNT->nextInScaf )
{
return 1;
}
CONNECT *cn_temp;
int count = 0;
if ( !contig_array[ctg].downwardConnect )
{
return count;
}
cn_temp = contig_array[ctg].downwardConnect;
while ( cn_temp )
{
if ( !cn_temp->deleted && !cn_temp->mask )
{
count++;
}
cn_temp = cn_temp->next;
}
return count;
}
/*************************************************
Function:
getNextContig
Description:
Gets the connection to next contig of current contig through constructed
connection in scaffold or direct connection to other contigs.
In the latter case, one and only one non-deleted and non-masked
connection is qualified.
Input:
1. ctg: current contig
2. preCNT: upstream connection of current contig
Output:
1. exception: indicate that whether found connection through
constructed connection in scaffold is deleted or masked
Return:
Pointer to qualified connection or NULL.
*************************************************/
static CONNECT *getNextContig ( unsigned int ctg, CONNECT *preCNT, boolean *exception )
{
CONNECT *cn_temp, *retCNT = NULL, *dh_cnt;
int count = 0, valid_in;
unsigned int nextCtg, bal_ctg;
*exception = 0;
if ( preCNT && preCNT->nextInScaf )
{
if ( preCNT->contigID != ctg )
{
fprintf ( stderr, "pre cnt does not lead to %d\n", ctg );
}
nextCtg = preCNT->nextInScaf->contigID;
cn_temp = getCntBetween ( ctg, nextCtg );
dh_cnt = getCntBetween ( getTwinCtg ( nextCtg ), getTwinCtg ( ctg ) );
if ( cn_temp && ( cn_temp->mask || cn_temp->deleted ) )
{
int id1 = 0, id2 = 0;
if ( dh_cnt->nextInScaf )
{
id1 = dh_cnt->nextInScaf->contigID;
id2 = getTwinCtg ( dh_cnt->nextInScaf->contigID );
}
if ( !cn_temp->prevInScaf )
{
fprintf ( stderr, "not even has a prevInScaf %d and %d, %d and %d with before %d with twin %d\n", ctg, nextCtg, getTwinCtg ( nextCtg ), getTwinCtg ( ctg ), id1, id2 );
}
cn_temp = getCntBetween ( getTwinCtg ( nextCtg ),
getTwinCtg ( ctg ) );
if ( !cn_temp->nextInScaf )
{
fprintf ( stderr, "its twin cnt not has a nextInScaf\n" );
}
fflush ( stdout );
*exception = 1;
}
else
{
return preCNT->nextInScaf;
}
}
bal_ctg = getTwinCtg ( ctg );
valid_in = validConnect ( bal_ctg, NULL );
if ( valid_in > 1 )
{
return NULL;
}
if ( !contig_array[ctg].downwardConnect )
{
return NULL;
}
cn_temp = contig_array[ctg].downwardConnect;
while ( cn_temp )
{
if ( cn_temp->mask || cn_temp->deleted )
{
cn_temp = cn_temp->next;
continue;
}
count++;
if ( count == 1 )
{
retCNT = cn_temp;
}
else if ( count == 2 )
{
return NULL;
}