static void sim4QueryOut(struct gfOutput *out, FILE *f)
/* Do sim4-like output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt = gab->axtList;
fprintf(f, "\n");
fprintf(f, "seq1 = %s, %d bp\n", axt->qName, gab->qSize);
fprintf(f, "seq2 = %s, %d bp\n", axt->tName, gab->tSize);
fprintf(f, "\n");
if (axt->qStrand == '-')
fprintf(f, "(complement)\n");
for (axt = gab->axtList; axt != NULL; axt = axt->next)
{
fprintf(f, "%d-%d ", axt->qStart+1, axt->qEnd);
fprintf(f, "(%d-%d) ", axt->tStart+1, axt->tEnd);
fprintf(f, "%1.0f%% ", 100.0 * axtIdRatio(axt));
if (axt->qStrand == '-')
fprintf(f, "<-\n");
else
fprintf(f, "->\n");
}
}
axtBundleFreeList(&aod->bundleList);
}
static void sim4QueryOut(struct gfOutput *out, FILE *f)
/* Do sim4-like output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
slReverse(&aod->bundleList);
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt = gab->axtList;
// check minIdentity of the entire alignment
int goodPpt = 1000 * axtListRatio(axt);
if (!(goodPpt >= out->minGood))
continue;
fprintf(f, "\n");
fprintf(f, "seq1 = %s, %d bp\n", axt->qName, gab->qSize);
fprintf(f, "seq2 = %s, %d bp\n", axt->tName, gab->tSize);
fprintf(f, "\n");
if (axt->qStrand == '-')
fprintf(f, "(complement)\n");
for (; axt != NULL; axt = axt->next)
{
fprintf(f, "%d-%d ", axt->qStart+1, axt->qEnd);
fprintf(f, "(%d-%d) ", axt->tStart+1, axt->tEnd);
fprintf(f, "%1.0f%% ", 100.0 * axtIdRatio(axt));
if (axt->qStrand == '-')
fprintf(f, "<-\n");
else
fprintf(f, "->\n");
}
}
axtBundleFreeList(&aod->bundleList);
}
static void doAChain(struct chain *chain, struct nibTwoCache *tSeqCache, struct nibTwoCache *qSeqCache,
FILE *f)
/* Convert one chain to an axt. */
{
struct dnaSeq *qSeq = loadSeqStrand(qSeqCache, chain->qName, chain->qStart, chain->qEnd, chain->qStrand);
struct dnaSeq *tSeq = loadSeqStrand(tSeqCache, chain->tName, chain->tStart, chain->tEnd, '+');
struct axt *axtList= chainToAxt(chain, qSeq, chain->qStart, tSeq, chain->tStart, maxGap, BIGNUM);
struct axt *axt = NULL;
for (axt = axtList; axt != NULL; axt = axt->next)
{
double idRatio = axtIdRatio(axt);
if (minIdRatio <= idRatio)
{
if (bedOut)
bedWriteAxt(axt, chain->qSize, chain->tSize, idRatio, f);
else
axtWrite(axt, f);
}
}
axtFreeList(&axtList);
freeDnaSeq(&qSeq);
freeDnaSeq(&tSeq);
}
