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;
}
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);
}
