void wormFreeNt4Genome(struct nt4Seq ***pNt4Seq)
/* Free up packed worm genome. */
{
struct nt4Seq **seqs;
int i;
if ((seqs = *pNt4Seq) == NULL)
return;
for (i=0; i<ArraySize(chromIds); ++i)
freeNt4(&seqs[i]);
freez(pNt4Seq);
}
void freeGenome(struct nt4Seq ***pNt4Seq, char ***pChromNames, int chromCount)
/* Free up genome. */
{
int i;
struct nt4Seq **nt4s = *pNt4Seq;
for (i=0; i<chromCount; ++i)
{
freeNt4(&nt4s[i]);
}
freez(pNt4Seq);
freez(pChromNames);
}
void flyFreeNt4Genome(struct nt4Seq ***pNt4Seq)
/* Free up packed fly genome. */
{
struct nt4Seq **pSeq;
int i;
if ((pSeq = *pNt4Seq) == NULL)
return;
for (i=0; i<ArraySize(ntFileNames); ++i)
freeNt4(&pSeq[i]);
freez(pNt4Seq);
}
void firstPass(char *aList, char *bList, char *outName)
/* Do first pass - find areas of homology between a and b,
* save to outName. */
{
char *aNameBuf, **aNames;
char *bNameBuf, **bNames;
int aCount, bCount;
struct nt4Seq **bNts, *bNt, *bNtList = NULL;
int bNtCount;
int i;
FILE *out = mustOpen(outName, "w");
/* Read in fa file lists . */
readAllWordsOrFa(aList, &aNames, &aCount, &aNameBuf);
readAllWordsOrFa(bList, &bNames, &bCount, &bNameBuf);
/* Convert second list to nt4 (packed) format in memory. */
printf("Loading and packing dna in %s\n", bList);
for (i=0; i<bCount; ++i)
{
char *bName = bNames[i];
struct dnaSeq *seqList, *seq;
seqList = faReadAllDna(bName);
for (seq = seqList; seq != NULL; seq = seq->next)
{
char uniqName[512];
sprintf(uniqName, "%s@%s", seq->name, bName);
bNt = newNt4(seq->dna, seq->size, uniqName);
slAddHead(&bNtList, bNt);
}
freeDnaSeqList(&seqList);
}
slReverse(&bNtList);
bNtCount = slCount(bNtList);
AllocArray(bNts, bNtCount);
for (i=0, bNt=bNtList; i<bNtCount; ++i, bNt=bNt->next)
bNts[i] = bNt;
printf("Loaded %d contigs from %d files\n", bNtCount, bCount);
/* Align elements of A list one at a time against B list. */
for (i=0; i<aCount; ++i)
{
char *aName = aNames[i];
struct dnaSeq *seqList, *seq;
printf("Aligning %s against %s\n", aName, bList);
seqList = faReadAllDna(aName);
for (seq = seqList; seq != NULL; seq = seq->next)
{
doCrude(aName, seq, bNts, bNtCount, out);
}
printf("\n");
freeDnaSeqList(&seqList);
}
/* Cleanup time. */
for (i=0; i<bNtCount; ++i)
freeNt4(&bNts[i]);
freeMem(bNts);
freeMem(aNames);
freeMem(bNames);
freeMem(aNameBuf);
freeMem(bNameBuf);
fclose(out);
}
