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);
}
int filterByQual(char *faFileName, FILE *f, int minQual, int minQualRun, struct hash *uniqHash)
/* Write out parts of sequence that meet quality standards to fa file in out.
* Returns untrimmed size. */
{
char qaFileName[512], dir[256], name[128], ext[64];
struct qaSeq *qa;
int start, size;
int initialSize;
splitPath(faFileName, dir, name, ext);
sprintf(qaFileName, "%s%s.qual", dir, name);
qa = qaMustReadBoth(qaFileName, faFileName);
if (hashLookup(uniqHash, qa->name))
warn("%s duplicated, ignoring all but first occurence", qa->name);
else
{
hashAdd(uniqHash, qa->name, NULL);
if (trimQa(qa, minQual, minQualRun, &start, &size))
{
faWriteNext(f, qa->name, qa->dna + start, size);
}
}
initialSize = qa->size;
qaSeqFree(&qa);
return initialSize;
}
void qaSeqFreeList(struct qaSeq **pList)
/* Free a list of QA seq's. */
{
struct qaSeq *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
qaSeqFree(&el);
}
*pList = NULL;
}
void qaToQac(char *inName, char *outName)
/* qaToQac - convert from uncompressed to compressed
* quality score format. */
{
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "wb");
struct qaSeq *qa;
qacWriteHead(f);
while ((qa = qaReadNext(lf)) != NULL)
{
qacWriteNext(f, qa);
qaSeqFree(&qa);
}
lineFileClose(&lf);
fclose(f);
}
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);
}
