int main(int argc, char *argv[])
/* Check parameters, set up, loop through each GenBank file. */
{
char *gbName;
int argi = 1;
struct hash *estAuthorHash = NULL;
char *pepFa;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
gByAccPrefixSize = optionInt("byAccPrefix", 0);
gbIdxName = optionVal("gbidx", NULL);
pepFa = optionVal("pepFa", NULL);
gbType = gbParseType(optionVal("type", "mrna,est"));
gbOrg = optionVal("org", NULL);
inclXMs = optionExists("inclXMs");
if (gByAccPrefixSize > 4) /* keep small to avoid tons of open files */
errAbort("max value of -byAccPrefix is 4");
gCurAccPrefix[0] = '\0';
faName = argv[argi++];
raName = argv[argi++];
estAuthorHash = newHash(23);
kvt = newKvt(5*1024);
gbfInit();
if (pepFa != NULL)
gPepFa = gbFaOpen(pepFa,"w");
char *blackList = optionVal("blackList", NULL);
if (blackList != NULL)
blackListRanges = genbankBlackListParse(blackList);
while (argi < argc)
{
gbName = argv[argi++];
printf("Processing %s into %s and %s\n", gbName, faName, raName);
procOneGbFile(gbName, estAuthorHash);
}
gbFaClose(&faFile);
gbFaClose(&gPepFa);
carefulClose(&raFile);
carefulClose(&gbIdxFile);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (optionExists("algoHelp"))
prAlgo();
if (argc != 3)
usage("wrong # of args");
gLocalNearBest = optionFrac("localNearBest", gLocalNearBest);
gGlobalNearBest = optionFrac("globalNearBest", gGlobalNearBest);
if ((gLocalNearBest >= 0.0) && (gGlobalNearBest >= 0.0))
errAbort("can only specify one of -localNearBest and -globalNearBest");
if (optionExists("usePolyTHead"))
gCDnaOpts |= cDnaUsePolyTHead;
if (optionExists("ignoreNs"))
gCDnaOpts |= cDnaIgnoreNs;
if (optionExists("ignoreIntrons"))
gCDnaOpts |= cDnaIgnoreIntrons;
if (optionExists("repsAsMatch"))
gCDnaOpts |= cDnaRepsAsMatch;
gMinId = optionFrac("minId", gMinId);
gMinCover = optionFrac("minCover", gMinCover);
gMinSpan = optionFrac("minSpan", gMinSpan);
gMinQSize = optionInt("minQSize", gMinQSize);
gMaxAligns = optionInt("maxAligns", gMaxAligns);
gMaxAlignsDrop = optionInt("maxAlignsDrop", gMaxAlignsDrop);
if ((gMaxAligns >= 0) && (gMaxAlignsDrop >= 0))
errAbort("cannot specify both -maxAligns and -maxAlignsDrop");
gMinAlnSize = optionInt("minAlnSize", gMinAlnSize);
gMinNonRepSize = optionInt("minNonRepSize", gMinNonRepSize);
gMaxRepMatch = optionFrac("maxRepMatch", gMaxRepMatch);
gPolyASizes = optionVal("polyASizes", NULL);
if (optionExists("usePolyTHead") && (gPolyASizes == NULL))
errAbort("must specify -polyASizes with -usePolyTHead");
gHapRegions = optionVal("hapRegions", NULL);
gBestOverlap = optionExists("bestOverlap");
gDropped = optionVal("dropped", NULL);
gWeirdOverlappped = optionVal("weirdOverlapped", NULL);
gFilterWeirdOverlapped = optionExists("filterWeirdOverlapped");
gHapRefMapped = optionVal("hapRefMapped", NULL);
gHapRefCDnaAlns = optionVal("hapRefCDnaAlns", NULL);
gHapLociAlns = optionVal("hapLociAlns", NULL);
if (optionExists("noValidate"))
gValidate = FALSE;
cDnaAlignsAlnIdQNameMode = optionExists("alnIdQNameMode");
if (optionExists("ignoreNs"))
gCDnaOpts |= cDnaIgnoreNs;
gUniqueMapped = optionExists("uniqueMapped");
gDecayMinCover = optionExists("decayMinCover");
char *blackList = optionVal("blackList", NULL);
if (blackList != NULL)
gBlackListRanges = genbankBlackListParse(blackList);
if ( gDecayMinCover && (gMinCover > 0.0))
errAbort("can only specify one of -minCoverage and -decayMinCoverage");
pslCDnaFilter(argv[1], argv[2]);
return 0;
}
