");
puts(liftOverErrHelp());
//system("/usr/bin/cal");
puts("");
return;
}
/* Get data to convert - from userData variable, or if
* that is empty from a file. */
if (cartOptionalString(cart, "SubmitFile"))
userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
else
userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
-dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT);
cartWebStart(cart, NULL, "Lift Genome Annotations");
getDbAndGenome(cart, &db, &organism, oldVars);
chainList = liftOverChainList();
choice = defaultChoices(chainList, db);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly\n");
minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
minChainT = cartCgiUsualInt(cart, HGLFT_MINCHAINT, choice->minChainT);
minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
-webMain(choice, dataFormat, multiple);
+webMain(choice, multiple);
liftOverChainFreeList(&chainList);
if (!refreshOnly && userData != NULL && userData[0] != '\0')
{
struct hash *chainHash = newHash(0);
char *chainFile;
struct tempName oldTn, mappedTn, unmappedTn;
FILE *old, *mapped, *unmapped;
char *line;
int lineSize;
char *fromDb, *toDb;
int ct = 0, errCt = 0;
/* read in user data and save to file */
makeTempName(&oldTn, HGLFT, ".user");
@@ -516,85 +490,67 @@
* for lines that could not be mapped */
makeTempName(&mappedTn, HGLFT, ".bed");
makeTempName(&unmappedTn, HGLFT, ".err");
mapped = mustOpen(mappedTn.forCgi, "w");
chmod(mappedTn.forCgi, 0666);
unmapped = mustOpen(unmappedTn.forCgi, "w");
chmod(unmappedTn.forCgi, 0666);
fromDb = cgiString(HGLFT_FROMDB_VAR);
toDb = cgiString(HGLFT_TODB_VAR);
chainFile = liftOverChainFile(fromDb, toDb);
if (chainFile == NULL)
errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
fromDb, toDb);
readLiftOverMap(chainFile, chainHash);
- if (sameString(dataFormat, WIGGLE_FORMAT))
- /* TODO: implement Wiggle */
- {}
- else if (sameString(dataFormat, POSITION_FORMAT))
- {
- ct = liftOverPositions(oldTn.forCgi, chainHash,
- minMatch, minBlocks, 0, minSizeQ,
- minChainT, 0,
- fudgeThick, mapped, unmapped, FALSE, NULL, &errCt);
-
-
- }
- else if (sameString(dataFormat, BED_FORMAT))
- {
- ct = liftOverBed(oldTn.forCgi, chainHash,
+ ct = liftOverBedOrPositions(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minChainT, 0,
fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
- }
- else
+ if (ct == -1)
/* programming error */
- errAbort("ERROR: Unsupported data format: %s\n", dataFormat);
+ errAbort("ERROR: Unsupported data format.\n");
webNewSection("Results");
- if (ct)
+ if (ct > 0)
{
/* some records succesfully converted */
cgiParagraph("");
printf("Successfully converted %d record", ct);
printf("%s: ", ct > 1 ? "s" : "");
printf("View Conversions\n", mappedTn.forCgi);
}
if (errCt)
{
/* some records not converted */
cgiParagraph("");
printf("Conversion failed on %d record", errCt);
printf("%s. ", errCt > 1 ? "s" : "");
printf("Display failure file \n",
unmappedTn.forCgi);
printf("Explain failure messages\n", HGLFT_ERRORHELP_VAR);
puts("Failed input regions:\n"); struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE); puts("
\n");
while (lineFileNext(errFile, &line, &lineSize))
puts(line);
lineFileClose(&errFile);
puts("\n");
- puts("Note: multiple checkbox ignored since it is not supported for position format.");
+ puts("Note: "multiple" option is not supported for position format.");
puts("