static void moveMeToFirst(struct mafAli *maf, char *myName)
/* Find component matching myName, and move it to first. */
{
struct mafComp *comp = mafMayFindCompPrefix(maf, myName, ".");
if (NULL == comp)
comp = mafFindCompPrefix(maf, myName, NULL);
slRemoveEl(&maf->components, comp);
slAddHead(&maf->components, comp);
}
struct mafComp *mafFindCompPrefix(struct mafAli *maf, char *pre, char *sep)
/* Find component of given source that starts with pre followed by sep
or die trying. */
{
struct mafComp *mc = mafMayFindCompPrefix(maf, pre, sep);
if (mc == NULL)
errAbort("Couldn't find %s%s... in maf", pre,sep);
return mc;
}
struct mafComp *mafMaster(struct mafAli *maf, struct mafFile *mf,
char *fileName)
/* Get master component from maf. Error abort if no master component */
{
struct mafComp *mcMaster = mafMayFindCompPrefix(maf, database, ".");
if (mcMaster == NULL)
{
errAbort("Couldn't find %s. sequence line %d of %s\n",
database, mf->lf->lineIx, fileName);
}
return mcMaster;
}
void fillHoles(struct mafAli *mafList, struct subSpecies *speciesList, struct twoBitFile *twoBit)
{
int lastEnd = 100000000;
struct mafAli *prevMaf = NULL, *maf, *nextMaf;
struct subSpecies *species;
/*
for(species = speciesList; species; species = species->next)
{
blockStatus = &species->blockStatus;
blockStatus->mc->rightStatus = MAF_NEW_STATUS;
blockStatus->mc->rightLen = 0;
}
*/
for(maf = mafList; maf ; prevMaf = maf, maf = nextMaf)
{
struct mafComp *mc = NULL, *masterMc, *lastMc = NULL;
struct mafAli *newMaf = NULL;
struct blockStatus *blockStatus;
nextMaf = maf->next;
masterMc=maf->components;
if (masterMc->start > lastEnd)
{
struct subSpecies *species;
for(species = speciesList; species; species = species->next)
{
mc = NULL;
// printf("looking at %s\n",species->name);
blockStatus = &species->blockStatus;
if (blockStatus->mc)
{
// printf("should match at %s\n",blockStatus->mc->src);
switch (blockStatus->mc->rightStatus)
{
case MAF_MISSING_STATUS:
//printf("missing right\n");
case MAF_NEW_NESTED_STATUS:
case MAF_MAYBE_NEW_NESTED_STATUS:
case MAF_CONTIG_STATUS:
case MAF_TANDEM_STATUS:
case MAF_INSERT_STATUS:
AllocVar(mc);
mc->rightStatus = mc->leftStatus = blockStatus->mc->rightStatus;
mc->rightLen = mc->leftLen = blockStatus->mc->rightLen;
mc->src = blockStatus->mc->src;
mc->srcSize = blockStatus->mc->srcSize;
mc->strand = blockStatus->mc->strand;
mc->start = blockStatus->mc->start + blockStatus->mc->size;
if (lastMc == NULL)
{
struct mafComp *miniMasterMc = NULL;
char *seqName;
struct dnaSeq *seq;
AllocVar(miniMasterMc);
miniMasterMc->next = mc;
miniMasterMc->strand = '+';
miniMasterMc->srcSize = masterMc->srcSize;
miniMasterMc->src = masterMc->src;
miniMasterMc->start = lastEnd;
miniMasterMc->size = masterMc->start - lastEnd;
if ((seqName = strchr(miniMasterMc->src, '.')) != NULL)
seqName++;
else
seqName = miniMasterMc->src;
// printf("hole filled from %d to %d\n",lastEnd, masterMc->start);
seq = twoBitReadSeqFrag(twoBit, seqName, lastEnd, masterMc->start);
miniMasterMc->text = seq->dna;
AllocVar(newMaf);
newMaf->textSize = maf->textSize;
newMaf->components = miniMasterMc;
newMaf->next = maf;
if (prevMaf)
prevMaf->next = newMaf;
else
mafList = newMaf;
//masterMc = miniMasterMc;
}
else
{
lastMc->next = mc;
}
lastMc = mc;
if (blockStatus->mc->rightStatus == MAF_MISSING_STATUS)
{
if (addN)
{
char buffer[256];
safef(buffer, sizeof(buffer), "%s.N",species->name);
mc->src = cloneString(buffer);
mc->start = 0;
mc->srcSize = 200000;
mc->size = masterMc->start - lastEnd;
mc->text = needMem(mc->size + 1);
memset(mc->text, 'N', mc->size);
}
}
else
{
if (addDash)
{
mc->size = masterMc->size;
mc->srcSize = blockStatus->mc->srcSize;
mc->text = needMem(mc->size + 1);
memset(mc->text, '-', mc->size);
mc->text[mc->size] = 0;
if (mc->size == 0)
errAbort("bad dash add");
mc->size = 0;
}
}
break;
}
}
}
}
lastEnd = masterMc->start + masterMc->size;
for(lastMc = masterMc; lastMc->next; lastMc = lastMc->next)
;
for(species = speciesList; species; species = species->next)
{
blockStatus = &species->blockStatus;
mc = NULL;
if ((blockStatus->masterStart <= masterMc->start) &&
(blockStatus->masterEnd > masterMc->start) &&
((mc = mafMayFindCompPrefix(maf, species->name,NULL)) == NULL))
{
if (blockStatus->mc != NULL)
{
switch (blockStatus->mc->rightStatus)
{
case MAF_MISSING_STATUS:
case MAF_CONTIG_STATUS:
case MAF_TANDEM_STATUS:
case MAF_INSERT_STATUS:
case MAF_NEW_NESTED_STATUS:
case MAF_MAYBE_NEW_NESTED_STATUS:
AllocVar(mc);
mc->rightStatus = mc->leftStatus = blockStatus->mc->rightStatus;
if (mc->rightStatus == MAF_NEW_NESTED_STATUS)
mc->rightStatus = MAF_INSERT_STATUS;
if (mc->leftStatus == MAF_NEW_NESTED_STATUS)
mc->leftStatus = MAF_INSERT_STATUS;
mc->rightLen = mc->leftLen = blockStatus->mc->rightLen;
mc->src = blockStatus->mc->src;
mc->strand = blockStatus->mc->strand;
mc->srcSize = blockStatus->mc->srcSize;
mc->start = blockStatus->mc->start + blockStatus->mc->size ;
lastMc->next = mc;
lastMc = mc;
if (addN && (blockStatus->mc->rightStatus == MAF_MISSING_STATUS))
{
char buffer[256];
safef(buffer, sizeof(buffer), "%s.N",species->name);
mc->src = cloneString(buffer);
mc->start = 0;
mc->srcSize = 200000;
mc->size = maf->textSize;
mc->text = needMem(mc->size + 1);
memset(mc->text, 'N', mc->size);
}
else if (addDash)
{
mc->size = masterMc->size;
mc->text = needMem(mc->size + 1);
if (mc->size == 0)
errAbort("bad dash add");
memset(mc->text, '-', mc->size);
mc->text[mc->size] = 0;
mc->size = 0;
}
break;
default:
break;
}
}
}
if (mc)
{
blockStatus->mc = mc;
}
}
}
}
void bridgeSpecies(struct mafAli *mafList, struct subSpecies *subSpecies)
{
struct mafAli *maf;
int pushState, leftLen;
struct mafComp *masterMc, *mc, *prevMc;
prevMc = mc = NULL;
for(; subSpecies; subSpecies = subSpecies->next)
{
//printf("bridging %s\n",subSpecies->name);
pushState = 0;
leftLen = 0;
for(maf = mafList; maf ; maf = maf->next)
{
masterMc = maf->components;
prevMc = mc;
if ((mc = mafMayFindCompPrefix(maf, subSpecies->name,NULL)) == NULL)
{
continue;
}
if (mc->leftStatus == 0)
errAbort("zero left status %s:%d\n",mc->src, mc->start);
#ifdef NOTNOW
if (pushState && (mc->leftStatus == MAF_INSERT_STATUS))
{
if (prevMc &&
!((prevMc->rightStatus == mc->leftStatus) &&
(prevMc->rightLen == mc->leftLen)))
{
printf("boo\n");
mc->leftStatus = MAF_NEW_NESTED_STATUS;
mc->leftLen = 0;
}
}
#endif
if (mc->leftStatus == MAF_NEW_STATUS)
{
if (pushState)
{
//printf("bridged on %s: %s:%d-%d\n",mc->src,"chr22",masterMc->start, masterMc->start + masterMc->size);
mc->leftStatus = MAF_NEW_NESTED_STATUS;
mc->leftLen = leftLen;
}
pushState++;
}
if (mc->rightStatus == 0)
{
errAbort("zero right status\n");
}
else if (isContigOrTandem(mc->rightStatus) || (mc->rightStatus == MAF_INSERT_STATUS))
leftLen = mc->rightLen;
else if (mc->rightStatus == MAF_NEW_STATUS)
{
pushState--;
if (pushState)
{
//printf("arched on %s: %s:%d-%d\n",mc->src,"chr22",masterMc->start, masterMc->start + masterMc->size);
mc->rightStatus = MAF_NEW_NESTED_STATUS;
mc->rightLen = leftLen;
}
}
}
//printf("pushState %d\n",pushState);
}
}
