int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeName = NULL;
optionHash(&argc, argv);
minScore = optionInt("minScore", minScore);
detailsName = optionVal("details", NULL);
gapFileName = optionVal("linearGap", NULL);
scoreSchemeName = optionVal("scoreScheme", NULL);
if (argc != 5)
usage();
if (scoreSchemeName != NULL)
{
verbose(1, "Reading scoring matrix from %s\n", scoreSchemeName);
scoreScheme = axtScoreSchemeRead(scoreSchemeName);
}
else
scoreScheme = axtScoreSchemeDefault();
dnaUtilOpen();
gapCalc = gapCalcReadOrDefault(gapFileName);
/* testGaps(); */
axtChain(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeFile = NULL;
optionHash(&argc, argv);
if (argc != 5)
usage();
if (optionExists("fa"))
{
qIsFa = TRUE;
qFaList = faReadAllMixed(argv[3]);
}
if (optionExists("tfa"))
{
tIsFa = TRUE;
tFaList = faReadAllMixed(argv[2]);
}
scoreSchemeFile = optionVal("scoreScheme", scoreSchemeFile);
if (scoreSchemeFile != NULL)
scoreScheme = axtScoreSchemeRead(scoreSchemeFile);
else
scoreScheme = axtScoreSchemeDefault();
lavToAxt(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeFile = NULL;
optionHash(&argc, argv);
if (argc != 3)
usage();
scoreSchemeFile = optionVal("scoreScheme", scoreSchemeFile);
if (scoreSchemeFile != NULL)
scoreScheme = axtScoreSchemeRead(scoreSchemeFile);
else
scoreScheme = axtScoreSchemeDefault();
axtRescore(argv[1], argv[2]);
return 0;
}
void subsetAxt(char *inName, char *outName, char *scoreFile, int threshold)
/* subsetAxt - Rescore alignments and output those over threshold. */
{
struct axtScoreScheme *ss = axtScoreSchemeRead(scoreFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct axt *axt;
if (threshold <= 0)
errAbort("Threshold must be a positive number");
while ((axt = axtRead(lf)) != NULL)
{
subsetOne(axt, ss, threshold, f);
axtFree(&axt);
axt = NULL;
}
}
int main(int argc, char *argv[])
{
char *scoreSchemeName = NULL;
optionHash(&argc, argv);
minScore = optionInt("minScore", minScore);
detailsName = optionVal("details", NULL);
gapFileName = optionVal("linearGap", NULL);
scoreSchemeName = optionVal("scoreScheme", NULL);
if (scoreSchemeName != NULL)
{
printf("Reading scoring matrix from %s\n", scoreSchemeName);
scoreScheme = axtScoreSchemeRead(scoreSchemeName);
}
else
scoreScheme = axtScoreSchemeDefault();
dnaUtilOpen();
initGapAid(gapFileName);
// testGaps();
if (argc != 5)
usage();
doChainScore(argv[1], argv[2], argv[3], argv[4]);
return 0;
}