struct qaSeq *qaRead(char *qaName)
/* Read in a .qa file (all records) or die trying. */
{
struct qaSeq *qa, *qaList = NULL;
if (isQacFile(qaName))
{
boolean isSwapped;
FILE *f = qacOpenVerify(qaName, &isSwapped);
while ((qa = qacReadNext(f, isSwapped)) != NULL)
{
slAddHead(&qaList, qa);
}
fclose(f);
}
else
{
struct lineFile *lf = lineFileOpen(qaName, TRUE);
while ((qa = qaReadNext(lf)) != NULL)
{
slAddHead(&qaList, qa);
}
lineFileClose(&lf);
}
slReverse(&qaList);
return qaList;
}
struct hash *qacReadToHash(char *fileName)
/* Read in a qac file into a hash of qacs keyed by name. */
{
boolean isSwapped;
FILE *f = qacOpenVerify(fileName, &isSwapped);
bits32 compSize, uncSize;
struct qac *qac;
char *name;
struct hash *hash = newHash(18);
int count = 0;
for (;;)
{
name = readString(f);
if (name == NULL)
break;
mustReadOne(f, uncSize);
if (isSwapped)
uncSize = byteSwap32(uncSize);
mustReadOne(f, compSize);
if (isSwapped)
compSize = byteSwap32(compSize);
qac = needHugeMem(sizeof(*qac) + compSize - 1);
qac->uncSize = uncSize;
qac->compSize = compSize;
mustRead(f, qac->data, compSize);
hashAdd(hash, name, qac);
++count;
}
carefulClose(&f);
printf("Read %d qacs from %s\n", count, fileName);
return hash;
}
void qacToWig(char *inName, char *outDir)
/* qacToWig - convert from compressed to wiggle format files in out dir */
{
boolean isSwapped;
FILE *in = qacOpenVerify(inName, &isSwapped);
FILE *out = NULL;
struct qaSeq *qa;
int outFileCount = 0;
if (fixed)
out = mustOpen(outDir, "wb");
else if (name == NULL)
makeDir(outDir);
while ((qa = qacReadNext(in, isSwapped)) != NULL)
{
if (name != NULL)
{
if (sameString(qa->name, name))
{
if (fixed)
wigFixedWrite(out, qa);
else
wigWrite(outDir, qa);
qaSeqFree(&qa);
outFileCount++;
break;
}
}
else if (fixed)
{
wigFixedWrite(out, qa);
qaSeqFree(&qa);
outFileCount = 1;
continue;
}
else
{
char outPath[1024];
safef(outPath, sizeof outPath, "%s/%s.wig", outDir, qa->name);
wigWrite(outPath, qa);
outFileCount++;
}
qaSeqFree(&qa);
}
carefulClose(&in);
if (fixed)
carefulClose(&out);
if (name == NULL)
verbose(1, "Made %d .wig files in %s\n", outFileCount, outDir);
else if (outFileCount < 1)
warn("Found no sequences with name \"%s\"\n", name);
}
static void fillInQac(char *qacName, struct hash *hash, struct qaSeq *qaList)
/* Hash contains qaSeq's with DNA sequence but no
* quality info. Fill in quality info from .qac file. */
{
boolean isSwapped;
FILE *f = qacOpenVerify(qacName, &isSwapped);
struct qaSeq *qa;
while ((qa = qacReadNext(f, isSwapped)) != NULL)
{
/* Transfer qa->qa to hash. */
attatchQaInfo(hash, qa->name, qa->qa, qa->size);
qa->qa = NULL;
qaSeqFree(&qa);
}
fclose(f);
checkAllPresent(qaList);
}
void qacToQa(char *inName, char *outName)
/* qacToQa - convert from compressed to uncompressed
* quality score format. */
{
boolean isSwapped;
FILE *in = qacOpenVerify(inName, &isSwapped);
FILE *out = mustOpen(outName, "wb");
struct qaSeq *qa;
int size = 0;
while ((qa = qacReadNext(in, isSwapped)) != NULL)
{
if (name != NULL)
if (!sameString(qa->name, name))
continue;
size += qa->size;
qaWriteNext(out, qa);
qaSeqFree(&qa);
}
verbose(3, "qa total size: %d\n", size);
fclose(in);
fclose(out);
}
