void
NDalign::realignForward(bool verbose, bool displayAlign) {
Match_Node_t match;
match.Start = abgn(); // Begin position in a
match.Offset = bbgn(); // Begin position in b
match.Len = 0;
match.Next = 0; // Not used here
int32 aLo=0, aHi=0;
int32 bLo=0, bHi=0;
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()--\n");
pedOverlapType olapType = _editDist->Extend_Alignment(&match, // Initial exact match, relative to start of string
_aStr, _aLen,
_bStr, _bLen,
aLo, aHi, // Output: Regions which the match extends
bLo, bHi);
aHi++; // Add one to the end point because Extend_Alignment returns the base-based coordinate.
bHi++;
// Is this a better overlap than what we have?
if (((score() < _editDist->score())) ||
((score() <= _editDist->score()) && (length() > ((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2))) {
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()-- Save better alignment - OLD length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
_bestResult.save(aLo, aHi, bLo, bHi, _editDist->score(), olapType, _editDist->Left_Delta_Len, _editDist->Left_Delta);
display("NDalign::realignForward()-- ", false);
_bestResult.setErate(1.0 - (double)(_matches + _gapmatches) / (length() - _freegaps));
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()-- Save better alignment - NEW length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
}
else if (displayAlign) {
fprintf(stderr, "NDalign::realignForward()-- Alignment no better - OLD length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
fprintf(stderr, "NDalign::realignForward()-- Alignment no better - NEW length %u erate %f score %u (%d-%d %d-%d)\n",
((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2, 0.0, _editDist->score(), aLo, aHi, bLo, bHi);
//display("NDalign::realignForward(NB)--", aLo, aHi, bLo, bHi, _editDist->Left_Delta, _editDist->Left_Delta_Len, true, false);
}
}
char *
ovOverlap::toString(char *str,
ovOverlapDisplayType type,
bool newLine) {
switch (type) {
case ovOverlapAsHangs:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_S32P" %6"F_U32P" %6"F_S32P" %7.6f%s%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
a_hang(), span(), b_hang(),
erate(),
(overlapIsDovetail()) ? "" : " PARTIAL",
(newLine) ? "\n" : "");
break;
case ovOverlapAsCoords:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %7.6f%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
span(),
a_bgn(), a_end(),
b_bgn(), b_end(),
erate(),
(newLine) ? "\n" : "");
break;
case ovOverlapAsRaw:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %7.6f %s %s %s%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
span(),
dat.ovl.ahg5, dat.ovl.ahg3,
dat.ovl.bhg5, dat.ovl.bhg3,
erate(),
dat.ovl.forOBT ? "OBT" : " ",
dat.ovl.forDUP ? "DUP" : " ",
dat.ovl.forUTG ? "UTG" : " ",
(newLine) ? "\n" : "");
break;
case ovOverlapAsCompat:
sprintf(str, "%8"F_U32P" %8"F_U32P" %c %6d %6d %5.2f %5.2f%s",
a_iid,
b_iid,
dat.ovl.flipped ? 'I' : 'N',
a_hang(), b_hang(),
erate() * 100.0,
erate() * 100.0,
(newLine) ? "\n" : "");
break;
case ovOverlapAsPaf:
// miniasm/map expects entries to be separated by tabs
// no padding spaces on names we don't confuse read identifiers
sprintf(str, "%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%c\t%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P" %s",
a_iid,
(g->gkStore_getRead(a_iid)->gkRead_sequenceLength()), a_bgn(), a_end(),
flipped() ? '-' : '+',
b_iid,
(g->gkStore_getRead(b_iid)->gkRead_sequenceLength()), flipped() ? b_end() : b_bgn(), flipped() ? b_bgn() : b_end(),
(uint32)floor(span() == 0 ? (1-erate() * (a_end()-a_bgn())) : (1-erate()) * span()),
span() == 0 ? a_end() - a_bgn() : span(),
255,
(newLine) ? "\n" : "");
break;
}
return(str);
}
bool
NDalign::processHits(void) {
// If the first time here, set the hit iterator to zero, otherwise move to the next one.
// And then return if there are no more hits to iterate over.
if (_hitr == UINT32_MAX)
_hitr = 0;
else
_hitr++;
if (_hitr >= _hits.size())
return(false);
// While hits, process them.
//
// If a good hit is found, return, leaving hitr as is. The next time we enter this function,
// we'll increment hitr and process the next hit. If no good hit is found, we iterate the loop
// until a good one is found, or we run out of hits.
for (; _hitr < _hits.size(); _hitr++) {
Match_Node_t match;
match.Start = _hits[_hitr].aBgn; // Begin position in a
match.Offset = _hits[_hitr].bBgn; // Begin position in b
match.Len = _hits[_hitr].tLen; // tLen can include mismatches if alternate scoring is used!
match.Next = 0; // Not used here
#ifdef SEED_NON_OVERLAPPING
match.Offset = _merSize; // Really should track this in the hits, oh well.
#endif
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "\n");
fprintf(stderr, "NDalign::processHits()-- Extend_Alignment Astart %d Bstart %d length %d\n", match.Start, match.Offset, match.Len);
#endif
int32 aLo=0, aHi=0;
int32 bLo=0, bHi=0;
pedOverlapType olapType = _editDist->Extend_Alignment(&match, // Initial exact match, relative to start of string
_aStr, _aLen,
_bStr, _bLen,
aLo, aHi, // Output: Regions which the match extends
bLo, bHi);
aHi++; // Add one to the end point because Extend_Alignment returns the base-based coordinate.
bHi++;
// Is this a better overlap than what we have? Save it and update statistics.
if (((score() < _editDist->score())) ||
((score() <= _editDist->score()) && (length() > ((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2))) {
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- Save better alignment - OLD length %u erate %f score %u (%d-%d %d-%d) ",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
#endif
_bestResult.save(aLo, aHi, bLo, bHi, _editDist->score(), olapType, _editDist->Left_Delta_Len, _editDist->Left_Delta);
display("NDalign::processHits()-- ", false);
_bestResult.setErate(1.0 - (double)(_matches + _gapmatches) / (length() - _freegaps));
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- NEW length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
#endif
} else {
olapType = pedBothBranch;
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- DON'T save alignment - OLD length %u erate %f score %u (%d-%d %d-%d) ",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
fprintf(stderr, "NDalign::processHits()-- NEW length %u score %u coords %u-%u %u-%u\n",
((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2,
_editDist->score(),
aLo, aHi, bLo, bHi);
#endif
}
// If a dovetail, we're done. Let the client figure out if the quality is good.
if (olapType == pedDovetail)
return(true);
} // Over all seeds.
// No more seeds to align. Did we save an alignment?
return(score() > 0);
}
