AS_CGB_Bubble_List_t
_collect_bubbles(BubGraph_t bg, BubVertexSet *fwd, BubVertexSet *rvs,
IntFragment_ID *top, int num_valid)
{
IntFragment_ID f, bub_start;
HashTable_AS *init_nodes = NULL;
IntFragment_ID *i_node = NULL;
AS_CGB_Bubble_List result;
AS_CGB_Bubble_List_t *ins_h = &(result.next);
BVSPair *bp_ins_keys = NULL, bp_find_key;
memset(&result,0,sizeof(AS_CGB_Bubble_List));
init_nodes = CreateGenericHashTable_AS(_hash_vset_hash, _hash_vset_cmp);
bp_ins_keys = (BVSPair *)safe_malloc(sizeof(BVSPair) * num_valid );
result.next = NULL;
for (f = 0; f < num_valid; ++f)
if (_is_initiation_node(BG_inDegree(bg, top[f], AS_CGB_BUBBLE_E_VALID),
BG_outDegree(bg, top[f], AS_CGB_BUBBLE_E_VALID)) &&
!BVS_empty(&(fwd[top[f]])) &&
!BVS_empty(&(rvs[top[f]]))) {
#if AS_CGB_BUBBLE_VERY_VERBOSE
fprintf(stderr, "Inserting "F_IID " ("F_IID ") into the table.\n", top[f],
get_iid_fragment(BG_vertices(bg), top[f]));
#endif
bp_ins_keys[f].f = &(fwd[top[f]]);
bp_ins_keys[f].r = &(rvs[top[f]]);
InsertInHashTable_AS(init_nodes, (uint64)(INTPTR)&bp_ins_keys[f], sizeof(BVSPair), (uint64)(INTPTR)&top[f], 0);
}
for (f = 0; f < num_valid; ++f)
if (_is_termination_node(BG_inDegree(bg, top[f], AS_CGB_BUBBLE_E_VALID),
BG_outDegree(bg, top[f], AS_CGB_BUBBLE_E_VALID))&&
!BVS_empty(&(fwd[top[f]])) &&
!BVS_empty(&(rvs[top[f]]))) {
#if AS_CGB_BUBBLE_VERY_VERBOSE
fprintf(stderr, "Looking for matches for "F_IID " ("F_IID ") in the table. ",
top[f], get_iid_fragment(BG_vertices(bg), top[f]));
#endif
bp_find_key.f = &(fwd[top[f]]);
bp_find_key.r = &(rvs[top[f]]);
i_node = (IntFragment_ID *)(INTPTR)LookupValueInHashTable_AS(init_nodes, (uint64)(INTPTR)&bp_find_key, sizeof(BVSPair));
#if AS_CGB_BUBBLE_VERY_VERBOSE
if (!i_node)
fprintf(stderr, "None found.\n");
else
fprintf(stderr, "Found init node = "F_IID " ("F_IID ").\n", *i_node,
get_iid_fragment(BG_vertices(bg), *i_node));
#endif
if (i_node) {
AS_CGB_Bubble_List_t new_bub = NULL;
new_bub = (AS_CGB_Bubble_List *)safe_malloc(sizeof(AS_CGB_Bubble_List));
bub_start = *i_node;
new_bub->start = bub_start;
new_bub->end = top[f];
*ins_h = new_bub;
ins_h = &(new_bub->next);
*ins_h = NULL;
}
}
DeleteHashTable_AS(init_nodes);
safe_free(bp_ins_keys);
return result.next;
}
int
updateFragmentWithParent(IntUnitigMesg *iunitig, int thisFrag, OverlapStore *ovs) {
uint32 ovlMax = 0;
uint32 ovlLen = 0;
OVSoverlap *ovl = NULL;
int testFrag = thisFrag - 1;
int testOvl = 0;
int oldParent = iunitig->f_list[thisFrag].parent;
int oldAHang = iunitig->f_list[thisFrag].ahang;
int oldBHang = iunitig->f_list[thisFrag].bhang;
uint32 consensusCutoff = AS_OVS_encodeQuality(AS_CNS_ERROR_RATE);
int contained = 0;
int fragment = -1;
int overlap = -1;
int overlapIdentity = consensusCutoff;
int overlapBHang = AS_READ_MAX_NORMAL_LEN;
HashTable_AS *ovlBefore = CreateScalarHashTable_AS();
HashTable_AS *ovlAfter = CreateScalarHashTable_AS();
HashTable_AS *iidIndex = CreateScalarHashTable_AS();
int hangSlop = 0;
int failed = -1;
fprintf(stderr, "\n");
fprintf(stderr, "WORKING on fragment %d == %d\n", thisFrag, iunitig->f_list[thisFrag].ident);
// Save in the hash table the fragments before/after this one.
//
for (testFrag=0; testFrag<iunitig->num_frags; testFrag++) {
InsertInHashTable_AS(iidIndex,
(uint64)iunitig->f_list[testFrag].ident, sizeof(uint64),
(uint64)testFrag, 0);
if (testFrag < thisFrag)
InsertInHashTable_AS(ovlBefore,
(uint64)iunitig->f_list[testFrag].ident, sizeof(uint64),
~(uint64)0, 0);
if (testFrag > thisFrag)
InsertInHashTable_AS(ovlAfter,
(uint64)iunitig->f_list[testFrag].ident, sizeof(uint64),
~(uint64)0, 0);
}
// Get the overlaps for this fragment.
//
AS_OVS_setRangeOverlapStore(ovs, iunitig->f_list[thisFrag].ident, iunitig->f_list[thisFrag].ident);
if (ovlMax < AS_OVS_numOverlapsInRange(ovs)) {
ovlMax = AS_OVS_numOverlapsInRange(ovs) * 2;
ovl = (OVSoverlap *)safe_realloc(ovl, sizeof(OVSoverlap) * ovlMax);
}
ovlLen = 0;
while (AS_OVS_readOverlapFromStore(ovs, ovl+ovlLen, AS_OVS_TYPE_OVL)) {
int aid=0, bid=0;
int afwd=0, bfwd=0;
int correct=0;
// Reorient the overlap so the b_iid is thisFrag.
//
{
AS_IID x = ovl[ovlLen].a_iid;
ovl[ovlLen].a_iid = ovl[ovlLen].b_iid;
ovl[ovlLen].b_iid = x;
if (ovl[ovlLen].dat.ovl.flipped) {
int x = ovl[ovlLen].dat.ovl.a_hang;
ovl[ovlLen].dat.ovl.a_hang = ovl[ovlLen].dat.ovl.b_hang;
ovl[ovlLen].dat.ovl.b_hang = x;
} else {
ovl[ovlLen].dat.ovl.a_hang = -ovl[ovlLen].dat.ovl.a_hang;
ovl[ovlLen].dat.ovl.b_hang = -ovl[ovlLen].dat.ovl.b_hang;
}
}
// Make sure we get the correct overlap. We seem to be allowed
// to have both an I and an N overlap for a given pair of
// fragments. At least, I hope that's all we're allowed.
//
aid = LookupValueInHashTable_AS(iidIndex, (uint64)ovl[ovlLen].a_iid, sizeof(uint64));
bid = LookupValueInHashTable_AS(iidIndex, (uint64)ovl[ovlLen].b_iid, sizeof(uint64));
afwd = (iunitig->f_list[aid].position.bgn < iunitig->f_list[aid].position.end);
bfwd = (iunitig->f_list[bid].position.bgn < iunitig->f_list[bid].position.end);
if ((afwd == bfwd) && (ovl[ovlLen].dat.ovl.flipped == 0))
correct = 1;
if ((afwd != bfwd) && (ovl[ovlLen].dat.ovl.flipped == 1))
correct = 1;
if (ExistsInHashTable_AS(ovlBefore, (uint64)ovl[ovlLen].a_iid, sizeof(uint64))) {
if (correct)
ReplaceInHashTable_AS(ovlBefore,
(uint64)ovl[ovlLen].a_iid, sizeof(uint64),
(uint64)ovlLen, 0);
fprintf(stderr, "%s before overlap for %d (%c) to %d (%c) ("F_S64","F_S64",%c) at ovl position %d\n",
correct ? "save" : "skip",
ovl[ovlLen].a_iid, afwd ? 'F' : 'R',
ovl[ovlLen].b_iid, bfwd ? 'F' : 'R',
ovl[ovlLen].dat.ovl.a_hang,
ovl[ovlLen].dat.ovl.b_hang,
ovl[ovlLen].dat.ovl.flipped ? 'I' : 'N',
ovlLen);
}
if (ExistsInHashTable_AS(ovlAfter, (uint64)ovl[ovlLen].a_iid, sizeof(uint64))) {
if (correct)
ReplaceInHashTable_AS(ovlAfter,
(uint64)ovl[ovlLen].a_iid, sizeof(uint64),
(uint64)ovlLen, 0);
fprintf(stderr, "%s after overlap for %d (%c) to %d (%c) ("F_S64","F_S64",%c) at ovl position %d\n",
correct ? "save" : "skip",
ovl[ovlLen].a_iid, afwd ? 'F' : 'R',
ovl[ovlLen].b_iid, bfwd ? 'F' : 'R',
ovl[ovlLen].dat.ovl.a_hang,
ovl[ovlLen].dat.ovl.b_hang,
ovl[ovlLen].dat.ovl.flipped ? 'I' : 'N',
ovlLen);
}
ovlLen++;
}
tryAgain:
// See if we're contained in any of these overlaps.
if (overlap == -1) {
for (testFrag=thisFrag-1; testFrag>=0; testFrag--) {
if (ExistsInHashTable_AS(ovlBefore, (uint64)iunitig->f_list[testFrag].ident, sizeof(uint64))) {
testOvl = LookupValueInHashTable_AS(ovlBefore, (uint64)iunitig->f_list[testFrag].ident, sizeof(uint64));
// Fragment has no overlap
if (testOvl == -1)
continue;
fprintf(stderr, "found testFrag = %d testOvl = %d erates "F_U64" %u hang "F_S64" "F_S64" (CONTAIN) slop=%d\n",
testFrag, testOvl,
ovl[testOvl].dat.ovl.orig_erate, consensusCutoff,
ovl[testOvl].dat.ovl.a_hang,
ovl[testOvl].dat.ovl.b_hang,
hangSlop);
// Three if's for documentation:
// 1) If we're an overlap we care about
// 2) If we're a contained overlap
// 3) If we're better than what we've seen so far
// Then save the overlap
//
if (ovl[testOvl].dat.ovl.orig_erate < consensusCutoff) {
if ((ovl[testOvl].dat.ovl.a_hang >= -hangSlop) &&
(ovl[testOvl].dat.ovl.b_hang <= hangSlop)) {
if (ovl[testOvl].dat.ovl.orig_erate < overlapIdentity) {
contained = 1;
fragment = testFrag;
overlap = testOvl;
overlapBHang = 0;
overlapIdentity = ovl[testOvl].dat.ovl.orig_erate;
}
}
}
}
}
}
// If not contained, scan the overlaps again, looking for the
// thickest/bestest. This will be the overlap with the smallest a
// or b hang -- depending on the orientation of the parent
// fragment.
//
// Instead of working through overlaps, we work through fragments.
//
if (overlap == -1) {
for (testFrag=thisFrag-1; testFrag>=0; testFrag--) {
if (ExistsInHashTable_AS(ovlBefore, (uint64)iunitig->f_list[testFrag].ident, sizeof(uint64))) {
int ahang = 0;
int bhang = 0;
testOvl = LookupValueInHashTable_AS(ovlBefore, (uint64)iunitig->f_list[testFrag].ident, sizeof(uint64));
// Fragment has no overlap
if (testOvl == -1)
continue;
// Overlap is too noisy
if (ovl[testOvl].dat.ovl.orig_erate >= consensusCutoff)
continue;
if (iunitig->f_list[testFrag].position.bgn < iunitig->f_list[testFrag].position.end) {
ahang = ovl[testOvl].dat.ovl.a_hang;
bhang = ovl[testOvl].dat.ovl.b_hang;
} else {
ahang = -ovl[testOvl].dat.ovl.b_hang;
bhang = -ovl[testOvl].dat.ovl.a_hang;
}
// Overlap isn't dovetail -- negative ahang
if (ahang < 0)
continue;
// Overlap isn't dovetail -- containment
if (bhang < 0)
continue;
fprintf(stderr, "found testFrag = %d testOvl = %d erates "F_U64" %u hang "F_S64" "F_S64" (DOVETAIL) slop=%d\n",
testFrag, testOvl,
ovl[testOvl].dat.ovl.orig_erate, consensusCutoff,
ovl[testOvl].dat.ovl.a_hang,
ovl[testOvl].dat.ovl.b_hang,
hangSlop);
if (bhang < overlapBHang) {
contained = 0;
fragment = testFrag;
overlap = testOvl;
overlapIdentity = ovl[testOvl].dat.ovl.orig_erate;
overlapBHang = bhang;
}
}
}
}
// Now, if we have found the parent fragment, update.
//
if (overlap >= 0) {
testOvl = overlap;
testFrag = fragment;
iunitig->f_list[thisFrag].parent = ovl[testOvl].a_iid;
if (contained)
iunitig->f_list[thisFrag].contained = iunitig->f_list[thisFrag].parent;
else
iunitig->f_list[thisFrag].contained = 0;
// Reorient again based on the orientation of the testFrag.
//
if (iunitig->f_list[testFrag].position.bgn < iunitig->f_list[testFrag].position.end) {
// testFrag is forward
iunitig->f_list[thisFrag].ahang = ovl[testOvl].dat.ovl.a_hang;
iunitig->f_list[thisFrag].bhang = ovl[testOvl].dat.ovl.b_hang;
} else {
// testFrag is reverse
iunitig->f_list[thisFrag].ahang = -ovl[testOvl].dat.ovl.b_hang;
iunitig->f_list[thisFrag].bhang = -ovl[testOvl].dat.ovl.a_hang;
}
// Report we did something.
//
fprintf(stderr, "Updated fragment "F_IID" from "F_IID",%d,%d to "F_IID",%d,%d\n",
iunitig->f_list[thisFrag].ident,
oldParent,
oldAHang,
oldBHang,
iunitig->f_list[thisFrag].parent,
iunitig->f_list[thisFrag].ahang,
iunitig->f_list[thisFrag].bhang);
goto successfullyUpdated;
}
// Otherwise, try to find an overlap again, this time allowing a
// bit of slop in the hangs.
//
if (hangSlop == 0) {
hangSlop = 10;
goto tryAgain;
}
// Now, we're convinced there is no decent overlap between this
// fragment and any fragment before it.
//
// Scan forward for the first thing we overlap.
for (testFrag=thisFrag+1; testFrag < iunitig->num_frags; testFrag++) {
int ahang = 0;
int bhang = 0;
testOvl = LookupValueInHashTable_AS(ovlAfter, (uint64)iunitig->f_list[testFrag].ident, sizeof(uint64));
// Fragment has no overlap
if (testOvl == -1)
continue;
// Overlap is too noisy
if (ovl[testOvl].dat.ovl.orig_erate >= consensusCutoff)
continue;
if (iunitig->f_list[testFrag].position.bgn < iunitig->f_list[testFrag].position.end) {
ahang = ovl[testOvl].dat.ovl.a_hang;
bhang = ovl[testOvl].dat.ovl.b_hang;
} else {
ahang = -ovl[testOvl].dat.ovl.b_hang;
bhang = -ovl[testOvl].dat.ovl.a_hang;
}
// Don't allow negative ahangs. At all. This catches the case
// where the parent might be contained in us, and generally makes
// consensus happier.
//
// Don't allow empty hangs - this can lead to infinite loops
// where we keep swapping the same two fragments. OK, not
// infinite, since we eventually run out of stack space and
// crash.
//
if (ahang <= 0)
continue;
fprintf(stderr, "shifttest ovl=%d testFrag="F_IID" pos %d-%d thisFrag="F_IID" pos %d-%d hangs %d,%d\n",
testOvl,
iunitig->f_list[testFrag].ident,
iunitig->f_list[testFrag].position.bgn,
iunitig->f_list[testFrag].position.end,
iunitig->f_list[thisFrag].ident,
iunitig->f_list[thisFrag].position.bgn,
iunitig->f_list[thisFrag].position.end,
ahang, bhang);
IntMultiPos fragCopy = iunitig->f_list[thisFrag];
memmove(iunitig->f_list + thisFrag,
iunitig->f_list + thisFrag + 1,
sizeof(IntMultiPos) * (testFrag - thisFrag));
iunitig->f_list[testFrag] = fragCopy;
fprintf(stderr, "Shifted fragment "F_IID" from position %d to position %d\n",
iunitig->f_list[testFrag].ident,
thisFrag, testFrag);
// Since we moved things around, we must process the new fragment
// at 'thisFrag's location.
//
failed = updateFragmentWithParent(iunitig, thisFrag, ovs);
if (failed == -1)
goto successfullyUpdated;
break;
}
// And we failed. Good luck with this one.
//
fprintf(stderr, "Failed to update fragment "F_IID" from "F_IID",%d,%d.\n",
iunitig->f_list[thisFrag].ident,
oldParent,
oldAHang,
oldBHang);
failed = thisFrag;
successfullyUpdated:
DeleteHashTable_AS(ovlBefore);
DeleteHashTable_AS(ovlAfter);
safe_free(ovl);
return(failed);
}
static
void
PlaceFragments(int32 fid,
IntUnitigPos *aiup,
CNS_Options *opp) {
Fragment *afrag = GetFragment(fragmentStore,fid);
Fragment *bfrag = NULL;
CNS_AlignedContigElement *belem = GetCNS_AlignedContigElement(fragment_positions, afrag->components);
if (afrag->n_components == 0)
return;
VA_TYPE(int32) *trace = CreateVA_int32(AS_READ_MAX_NORMAL_LEN+1);
for (; belem->frg_or_utg == CNS_ELEMENT_IS_FRAGMENT; belem++) {
if (FALSE == ExistsInHashTable_AS(fragmentMap, belem->idx.fragment.frgIdent, 0))
// Fragment is not in the contigs f_list. It is an unplaced read from a surrogate.
continue;
// if it exists in the fragmentMap it should exist in this map as well since it was added at the same time
// look up where this fragment is placed within the entire contig, see if that matches where we're about to place it
// this is necessary for surrogates that are multiply placed in a single contig for example:
// contig: --------------*****--------*****--------> where ***** represents a surrogate
// ----> readA
// when placing readA within the surrogate unitig, we see if readA belongs in surrogate instance A or B
// by computing the position of the unitig within the contig and adding ahang to it
// if this computed position matches the position that the IMP record retrieved below tells us, proceed, otherwise skip placement
IntMultiPos *bimp = (IntMultiPos *)LookupValueInHashTable_AS(fragmentToIMP, belem->idx.fragment.frgIdent, 0);
int32 bbgn = (bimp->position.bgn < bimp->position.end ? bimp->position.bgn : bimp->position.end);
int32 abgn = (aiup->position.bgn < aiup->position.end ? aiup->position.bgn : aiup->position.end);
int32 fcomplement = afrag->complement;
int32 bcomplement = (belem->position.bgn < belem->position.end) ? 0 : 1;
int32 ahang = 0;
int32 bhang = 0;
int32 ovl = 0;
OverlapType otype;
// all of fid's component frags will be aligned to it (not to
// each other)
//
// fcomplement==0 fcomplement==1
//
// A) fid C) fid
// ------------------> <----------------
// ---> <---
// bid (bcomplement==0) bid
//
// B) fid D) fid
// ------------------> <----------------
// <--- --->
// bid (bcomplement==1) bid
//
// The afrag is a unitig, so b is always contained (length of
// overlap is length of belem).
if (fcomplement && bcomplement) {
ahang = afrag->length - belem->position.bgn; /* Case D */
bhang = belem->position.end - afrag->length;
ovl = belem->position.bgn - belem->position.end;
} else if (fcomplement && !bcomplement) {
ahang = afrag->length - belem->position.end; /* Case C */
bhang = belem->position.bgn - afrag->length;
ovl = belem->position.end - belem->position.bgn;
} else if (!fcomplement && bcomplement) {
ahang = belem->position.end; /* Case B */
bhang = belem->position.bgn - afrag->length;
ovl = belem->position.bgn - belem->position.end;
} else {
ahang = belem->position.bgn; /* Case A */
bhang = belem->position.end - afrag->length;
ovl = belem->position.end - belem->position.bgn;
}
assert(ahang >= 0);
assert(bhang <= 0);
assert(ovl > 0);
if (aiup->num_instances > 1 && abs(ahang + abgn - bbgn) > MAX_SURROGATE_FUDGE_FACTOR) {
if (VERBOSE_MULTIALIGN_OUTPUT)
fprintf(stderr, "Not placing fragment %d into unitig %d because the positions (%d, %d) do not match (%d, %d)\n",
belem->idx.fragment.frgIdent, afrag->iid,
bimp->position.bgn, bimp->position.end,
ahang + GetColumn(columnStore,(GetBead(beadStore,afrag->firstbead.get() ))->column_index)->ma_index,
bhang + GetColumn(columnStore,(GetBead(beadStore,afrag->firstbead.get()+afrag->length-1))->column_index)->ma_index+1);
continue;
}
int32 blid = AppendFragToLocalStore(belem->idx.fragment.frgType,
belem->idx.fragment.frgIdent,
(bcomplement != fcomplement),
belem->idx.fragment.frgContained,
AS_OTHER_UNITIG);
afrag = GetFragment(fragmentStore, fid); // AppendFragToLocalStore can change the pointer on us.
bfrag = GetFragment(fragmentStore, blid);
if (!GetAlignmentTraceDriver(afrag, NULL, bfrag, &ahang, &bhang, ovl, trace, &otype, GETALIGNTRACE_CONTIGF, 0)) {
//if (!GetAlignmentTrace(afrag->lid, 0, blid, &ahang, &bhang, ovl, trace, &otype, DP_Compare, DONT_SHOW_OLAP, 0, AS_CONSENSUS, AS_CNS_ERROR_RATE) &&
// !GetAlignmentTrace(afrag->lid, 0, blid, &ahang, &bhang, ovl, trace, &otype, Local_Overlap_AS_forCNS, DONT_SHOW_OLAP, 0, AS_CONSENSUS, AS_CNS_ERROR_RATE)) {
Bead *afirst = GetBead(beadStore, afrag->firstbead.get() + ahang);
Column *col = GetColumn(columnStore, afirst->column_index);
MANode *manode = GetMANode(manodeStore, col->ma_id);
RefreshMANode(manode->lid, 0, opp, NULL, NULL, 0, 0); // BPW not sure why we need this
fprintf(stderr, "Could (really) not find overlap between %d (%c) and %d (%c) estimated ahang: %d (ejecting frag %d from contig)\n",
afrag->iid, afrag->type, belem->idx.fragment.frgIdent, belem->idx.fragment.frgType, ahang, belem->idx.fragment.frgIdent);
GetFragment(fragmentStore,blid)->deleted = 1;
} else {
ApplyAlignment(afrag->lid, 0, NULL, blid, ahang, Getint32(trace,0));
}
} // over all fragments
Delete_VA(trace);
}
int main (int argc, char *argv[]) {
char *asmFileName = NULL;
char *tigStoreName = NULL;
uint32 tigStoreVers = 2;
int minLength = DEFAULT_UNITIG_LENGTH;
int numInstances = DEFAULT_NUM_INSTANCES;
int distanceToEnds = DEFAULT_DISTANCE_TO_ENDS;
uint32 numToggled = 0;
argc = AS_configure(argc, argv);
int arg=1;
int err=0;
while (arg < argc) {
if (strcmp(argv[arg], "-a") == 0) {
asmFileName = argv[++arg];
} else if (strcmp(argv[arg], "-t") == 0) {
tigStoreName = argv[++arg];
tigStoreVers = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-l") == 0) {
minLength = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-n") == 0) {
numInstances = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-d") == 0) {
distanceToEnds = atoi(argv[++arg]);
} else {
fprintf(stderr, "%s: unknown option '%s'\n", argv[0], argv[arg]);
err++;
}
arg++;
}
if (minLength <= 0) err++;
if (numInstances < 0) err++;
if (distanceToEnds <= 0) err++;
if ((asmFileName == NULL) || (tigStoreName == NULL) || (err > 0)) {
fprintf(stderr, "usage: %s -a asmFile -t tigStore version [-l minLength] [-n numInstances] [-d distanceToEnd]\n", argv[0]);
fprintf(stderr, "\n");
fprintf(stderr, " -a asmFile path to the assembly .asm file\n");
fprintf(stderr, " -t tigStore version path to the tigStore and version to modify\n");
fprintf(stderr, " -l minLength minimum size of a unitig to be toggled, default=%d)\n", DEFAULT_UNITIG_LENGTH);
fprintf(stderr, " -n numInstances number of instances of a surrogate that is toggled, default = %d\n", DEFAULT_NUM_INSTANCES);
fprintf(stderr, " -d distanceToEnd max number of bases the surrogate can be from the end of a scaffold for toggling, default = %d\n", DEFAULT_DISTANCE_TO_ENDS);
fprintf(stderr, "\n");
fprintf(stderr, " Labels surrogate unitigs as non-repeat if they match any of the following conditions:\n");
fprintf(stderr, " 1. the unitig meets all the -l, -n and -d conditions\n");
fprintf(stderr, " 2. When -n = 0, all surrogate unitigs with more than one read\n");
fprintf(stderr, " 3. the unitig appears exactly twice, within '-d' bases from the end of a scaffold\n");
exit(1);
}
HashTable_AS *UIDtoIID = CreateScalarHashTable_AS();
HashTable_AS *CTGtoFirstUTG = CreateScalarHashTable_AS();
HashTable_AS *CTGtoLastUTG = CreateScalarHashTable_AS();
VA_TYPE(int32) *unitigLength = CreateVA_int32(8192);
VA_TYPE(uint32) *surrogateCount = CreateVA_uint32(8192);
VA_TYPE(uint32) *surrogateAtScaffoldEnds = CreateVA_uint32(8192);
GenericMesg *pmesg;
FILE *infp = fopen(asmFileName, "r");
while ((EOF != ReadProtoMesg_AS(infp, &pmesg))) {
SnapUnitigMesg *utg = NULL;
SnapConConMesg *ctg = NULL;
SnapScaffoldMesg *scf = NULL;
uint32 count = 0;
uint32 forward = TRUE;
uint32 lastCtg = 0;
switch(pmesg->t) {
case MESG_UTG:
utg = (SnapUnitigMesg*)(pmesg->m);
Setint32(unitigLength, utg->iaccession, &utg->length);
if (utg->length >= minLength && (utg->status == AS_NOTREZ || utg->status == AS_SEP)) {
// store the mapping for this unitig's UID to IID and initialize it's instance counter at 0
count = 0;
InsertInHashTable_AS(UIDtoIID, AS_UID_toInteger(utg->eaccession), 0, (uint64)utg->iaccession, 0);
Setuint32(surrogateCount, utg->iaccession, &count);
}
break;
case MESG_CCO:
ctg = (SnapConConMesg *)(pmesg->m);
for (int32 i = 0; i < ctg->num_unitigs; i++) {
// increment the surrogate unitigs instance counter
if (ExistsInHashTable_AS(UIDtoIID, AS_UID_toInteger(ctg->unitigs[i].eident), 0)) {
uint32 *ret = Getuint32(surrogateCount, (uint32) LookupValueInHashTable_AS(UIDtoIID, AS_UID_toInteger(ctg->unitigs[i].eident), 0));
assert(ret != NULL);
(*ret)++;
// store first surrogate in a contig
if (!ExistsInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(ctg->eaccession), 0) &&
MIN(ctg->unitigs[i].position.bgn, ctg->unitigs[i].position.end) < distanceToEnds) {
InsertInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(ctg->eaccession), 0, LookupValueInHashTable_AS(UIDtoIID, AS_UID_toInteger(ctg->unitigs[i].eident), 0), 0);
}
// also store the last
if ((ctg->length - MAX(ctg->unitigs[i].position.bgn, ctg->unitigs[i].position.end)) < distanceToEnds) {
ReplaceInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(ctg->eaccession), 0, LookupValueInHashTable_AS(UIDtoIID, AS_UID_toInteger(ctg->unitigs[i].eident), 0), 0);
}
}
}
break;
case MESG_SCF:
scf = (SnapScaffoldMesg *)(pmesg->m);
count = scf->iaccession;
if (scf->contig_pairs[0].orient.isAnti() || scf->contig_pairs[0].orient.isOuttie()) {
forward = FALSE;
}
lastCtg = MAX(scf->num_contig_pairs - 1, 0);
// All four cases below follow the same pattern
// The first time a surrogate is found at the end of a scaffold, we record the scaffold ID
// When the surrogate is seen at the end of a second scaffold, we record that it has been found at the ends of two scaffolds (UINT32_MAX)
// If the surrogate is seen more than once in a single scaffold, it is eliminated (it can't connect two scaffolds)
// If the surrogate is only seen once at the end of a scaffold (and again in the middle), it is eliminated
// 1. Contig is first in scaffold and is forward, take the surrogate from the beginning of contig, if it exists
if (ExistsInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0) && forward) {
uint32 *myval = Getuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0));
if (myval != NULL && (*myval) == scf->iaccession) {
count = 0;
} else if (myval != NULL && (*myval) != 0 && (*myval) != scf->iaccession) {
count = UINT32_MAX;
}
Setuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0), &count);
count = scf->iaccession;
}
// 2. Contig is last in scaffold and is reversed, take the surrogate from the beginning of the contig, if it exists
if (ExistsInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0) && !forward) {
uint32 *myval = Getuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0));
if (myval != NULL && (*myval) == scf->iaccession) {
count = 0;
} else if (myval != NULL && (*myval) != 0 && (*myval) != scf->iaccession) {
count = UINT32_MAX;
}
Setuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoFirstUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0), &count);
count = scf->iaccession;
}
// 3. Contig is first in scaffold and is reversed, take the surrogate from the end of the contig, if it exists
if (ExistsInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0) && !forward) {
uint32 *myval = Getuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0));
if (myval != NULL && (*myval) == scf->iaccession) {
count = 0;
} else if (myval != NULL && (*myval) != 0 && (*myval) != scf->iaccession) {
count = UINT32_MAX;
}
Setuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[0].econtig1), 0), &count);
count = scf->iaccession;
}
// 4. Contig is last in scaffold and is forward, take the surrogate from the end of the contig, if it exists
if (ExistsInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0) && forward) {
uint32 *myval = Getuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0));
if (myval != NULL && (*myval) == scf->iaccession) {
count = 0;
} else if (myval != NULL && (*myval) != 0 && (*myval) != scf->iaccession) {
count = UINT32_MAX;
}
Setuint32(surrogateAtScaffoldEnds, (uint32) LookupValueInHashTable_AS(CTGtoLastUTG, AS_UID_toInteger(scf->contig_pairs[lastCtg].econtig2), 0), &count);
count = scf->iaccession;
}
break;
default:
break;
}
}
fclose(infp);
uint32 *ret = NULL;
uint32 *atScfEnd = NULL;
// open the tig store for in-place writing (we don't increment the version since CGW always reads a fixed version initially)
// this also removes any partitioning
MultiAlignStore *tigStore = new MultiAlignStore(tigStoreName, tigStoreVers, 0, 0, TRUE, TRUE);
for (uint32 i = 0; i < tigStore->numUnitigs(); i++) {
uint32 *ret = Getuint32(surrogateCount, i);
uint32 *atScfEnd = Getuint32(surrogateAtScaffoldEnds, i);
uint32 *length = Getuint32(unitigLength, i);
bool toggled = false;
if (ret != NULL && (*ret) == (uint32)numInstances && numInstances != 0) {
toggled = TRUE;
}
// if we find a surrogate that has two instances and it is at scaffold ends mark toggle it as well
else if (ret != NULL && (*ret) == NUM_INSTANCES_AT_SCAFFOLD_ENDS && atScfEnd != NULL && (*atScfEnd) == UINT32_MAX) {
toggled = TRUE;
}
// special case, mark non-singleton unitigs as unique if we are given no instances
else if (numInstances == 0 && (length != NULL && (*length) >= minLength) && tigStore->getNumFrags(i, TRUE) > 1) {
toggled = TRUE;
}
if (toggled) {
tigStore->setUnitigFUR(i, AS_FORCED_UNIQUE);
numToggled++;
}
}
DeleteHashTable_AS(UIDtoIID);
DeleteHashTable_AS(CTGtoFirstUTG);
DeleteHashTable_AS(CTGtoLastUTG);
delete tigStore;
fprintf(stderr, "Toggled %d\n", numToggled);
return 0;
}
