2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 braney Fri Apr 5 16:57:02 2024 -0700 ongoing work on quickLift diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c index c30b4dc..95e09ca 100644 --- src/hg/hgConvert/hgConvert.c +++ src/hg/hgConvert/hgConvert.c @@ -11,30 +11,32 @@ #include "hCommon.h" #include "fa.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "cart.h" #include "web.h" #include "chain.h" #include "liftOver.h" #include "liftOverChain.h" #include "chromInfo.h" #include "net.h" #include "genark.h" #include "trackHub.h" +#include "quickLift.h" +#include "exportedDataHubs.h" /* CGI Variables */ #define HGLFT_TOORG_VAR "hglft_toOrg" /* TO organism */ #define HGLFT_TODB_VAR "hglft_toDb" /* TO assembly */ #define HGLFT_DO_CONVERT "hglft_doConvert" /* Do the actual conversion */ /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static char *organism = NULL; static char *database = NULL; /* Javascript to support New Assembly pulldown when New Genome changes. */ /* Copies selected values to a hidden form */ @@ -46,67 +48,81 @@ struct dbDb *db; for (db = list; db != NULL; db = db->next) { if (sameString(name, db->name)) return db; } errAbort("Can't find %s in matchingDb", name); return NULL; } static void askForDestination(struct liftOverChain *liftOver, char *fromPos, struct dbDb *fromDb, struct dbDb *toDb) /* set up page for entering data */ { struct dbDb *dbList; +boolean askAboutQuickLift = FALSE; + +if (exportedDataHubsEnabled()) + askAboutQuickLift = TRUE; cartWebStart(cart, database, "Convert %s to New Assembly", fromPos); /* create HMTL form */ puts("
\n"); cartSaveSession(cart); /* create HTML table for layout purposes */ puts("\n\n"); /* top row -- labels */ cgiSimpleTableRowStart(); cgiTableField("Old Genome: "); cgiTableField("Old Assembly: "); cgiTableField("New Genome: "); cgiTableField("New Assembly: "); +if (askAboutQuickLift) + cgiTableField("QuickLift Tracks: "); cgiTableField(" "); cgiTableRowEnd(); /* Next row -- data and controls */ cgiSimpleTableRowStart(); /* From organism and assembly. */ cgiTableField(fromDb->organism); cgiTableField(fromDb->description); /* Destination organism. */ cgiSimpleTableFieldStart(); dbList = hGetLiftOverToDatabases(liftOver->fromDb); printSomeGenomeListHtmlNamed(HGLFT_TOORG_VAR, liftOver->toDb, dbList, "change", onChangeToOrg); cgiTableFieldEnd(); /* Destination assembly */ cgiSimpleTableFieldStart(); printAllAssemblyListHtmlParm(liftOver->toDb, dbList, HGLFT_TODB_VAR, TRUE, NULL, NULL); cgiTableFieldEnd(); +if (askAboutQuickLift) + { + cgiSimpleTableFieldStart(); + boolean quickLift = cartUsualBoolean(cart, "doQuickLift", FALSE); + cgiMakeCheckBoxWithId("doQuickLift", quickLift, "doQuickLift"); + cgiTableFieldEnd(); + } + cgiSimpleTableFieldStart(); cgiMakeButton(HGLFT_DO_CONVERT, "Submit"); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); puts("\n"); cartWebEnd(); } static double scoreLiftOverChain(struct liftOverChain *chain, char *fromOrg, char *fromDb, char *toOrg, char *toDb, struct hash *dbRank ) /* Score the chain in terms of best match for cart settings */ @@ -257,37 +273,56 @@ } slSort(&chainList, chainCmpScore); return chainList; } static void doConvert(char *fromPos) /* Actually do the conversion */ { struct dbDb *fromDb = hDbDb(trackHubSkipHubName(database)), *toDb = hDbDb(cartString(cart, HGLFT_TODB_VAR)); char *fileName = liftOverChainFile(fromDb->name, toDb->name); fileName = hReplaceGbdbMustDownload(fileName); char *chrom; int start, end; int origSize; struct chain *chainList, *chain; +struct dyString *visDy = NULL; cartWebStart(cart, database, "%s %s %s to %s %s", fromDb->organism, fromDb->description, fromPos, toDb->organism, toDb->description); if (!hgParseChromRange(database, fromPos, &chrom, &start, &end)) errAbort("position %s is not in chrom:start-end format", fromPos); origSize = end - start; +boolean doQuickLift = cartUsualBoolean(cart, "doQuickLift", FALSE); + +unsigned quickChain = 0; +unsigned quickHub = 0; + +if (doQuickLift) + { + quickChain = quickLiftGetChain(fromDb->name, toDb->name); + + if (quickChain == 0) + errAbort("can't find quickChain from %s to %s", fromDb->name, toDb->name); + + visDy = newDyString(1024); + char *newHub = trackHubBuild(fromDb->name, cart, visDy); + if ((quickHub = registerExportedDataHub(fromDb->name, newHub)) == 0) + errAbort("can't register exportedDataHub %s\n", newHub); + } + chainList = chainLoadAndTrimIntersecting(fileName, chrom, start, end); if (chainList == NULL) printf("Sorry this position couldn't be found in new assembly"); else { for (chain = chainList; chain != NULL; chain = chain->next) { int blockSize; int qStart, qEnd; if (chain->qStrand == '-') { qStart = chain->qSize - chain->qEnd; qEnd = chain->qSize - chain->qStart; } else @@ -297,40 +332,48 @@ } blockSize = chainTotalBlockSize(chain); /* Check if the toDb database exists and if the chromosome sequence file (of the hgConvert result) exists in the location specified in chromInfo for the toDb. */ boolean chromSeqExists = (sqlDatabaseExists(toDb->name) && chromSeqFileExists(toDb->name, chain->qName)); /* Check if the toDb has active set to 1 in dbDb if the toDb database exists. If these conditions are met then print position link to browser for toDb, otherwise just print position without link. */ boolean startedAnchor = FALSE; if ((hDbIsActive(toDb->name) && chromSeqExists) || startsWith("hub:",toDb->nibPath)) { + if (quickChain) + printf("", + hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain, visDy->string); + else printf("", hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd); startedAnchor = TRUE; } else if (sameString(toDb->nibPath, "genark")) { char *hubUrl = genarkUrl(toDb->name); if (hubUrl) { startedAnchor = TRUE; + if (quickChain) + printf("", + hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain); + else printf("", hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd); } } printf("%s:%d-%d", chain->qName, qStart+1, qEnd); if (startedAnchor) printf(""); printf(" (%3.1f%% of bases, %3.1f%% of span)
\n", 100.0 * blockSize/origSize, 100.0 * (chain->tEnd - chain->tStart) / origSize); } } cartWebEnd(); }