void rmskOut2OpenVerify(char *fileName, struct lineFile **retFile, boolean *retEmpty)
/* Open repeat masker .out file and verify that it is good.
* Set retEmpty if it has header characteristic of an empty file. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
int lineSize;
lineFileNeedNext(lf, &line, &lineSize);
if (startsWith("There were no", line))
*retEmpty = TRUE;
line = skipLeadingSpaces(line);
if (! ( startsWith("SW", line) || startsWith("bit", line) ) )
errAbort("%s doesn't seem to be a RepeatMasker .out file", fileName);
lineFileSkip(lf, 2);
*retEmpty = FALSE;
*retFile = lf;
}
struct hash *getFreqHash(char *freqFile)
/* Read the frequency file in, and store it in a hash and return that. */
{
struct hash *freqHash = newHash(23);
struct lineFile *lf = lineFileOpen(freqFile, TRUE);
char *words[3];
/* Assume there's a header and skip it. */
lineFileSkip(lf, 1);
while (lineFileRowTab(lf, words))
{
int val;
lineFileNeedFullNum(lf, words, 1);
lineFileNeedFullNum(lf, words, 2);
val = (int)sqlUnsigned(words[2]);
addFreqToHash(freqHash, words[0], words[1], val);
}
lineFileClose(&lf);
hashTraverseEls(freqHash, sortSlPairList);
return freqHash;
}
