void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { /* struct liftOverChain *chainList = NULL, *chain; */ char *userData; /* char *dataFile; */ char *dataFormat; char *organism; char *db; float minBlocks, minMatch; boolean multiple, fudgeThick; int minSizeQ, minSizeT; boolean refreshOnly = FALSE; /* char *err = NULL; */ struct liftOverChain *chainList = NULL, *choice; cart = theCart; if (cgiOptionalString(HGLFT_ERRORHELP_VAR)) { puts("<PRE>"); puts(liftOverErrHelp()); //system("/usr/bin/cal"); puts("</PRE>"); 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 = liftOverChainListFiltered(); choice = defaultChoices(chainList, db); if (choice == NULL) errAbort("Sorry, no conversions available from this assembly\n"); minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ); minSizeT = cartCgiUsualInt(cart, HGLFT_MINSIZET, choice->minSizeT); 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); 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"); old = mustOpen(oldTn.forCgi, "w"); fputs(userData, old); fputs("\n", old); /* in case user doesn't end last line */ carefulClose(&old); chmod(oldTn.forCgi, 0666); /* setup output files -- one for converted lines, the other * 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)) { /* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */ /* ignore multiple, it must be false when position is used */ ct = liftOverPositions(oldTn.forCgi, chainHash, minMatch, minBlocks, 0, minSizeQ, minSizeT, 0, fudgeThick, mapped, unmapped, FALSE, NULL, &errCt); } else if (sameString(dataFormat, BED_FORMAT)) { /* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */ ct = liftOverBed(oldTn.forCgi, chainHash, minMatch, minBlocks, 0, minSizeQ, minSizeT, 0, fudgeThick, mapped, unmapped, multiple, NULL, &errCt); } else /* programming error */ errAbort("ERROR: Unsupported data format: %s\n", dataFormat); webNewSection("Results"); if (ct) { /* some records succesfully converted */ cgiParagraph(""); printf("Successfully converted %d record", ct); printf("%s: ", ct > 1 ? "s" : ""); printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi); } if (errCt) { /* some records not converted */ cgiParagraph(""); printf("Conversion failed on %d record", errCt); printf("%s. ", errCt > 1 ? "s" : ""); printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n", unmappedTn.forCgi); printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR); puts("<P>Failed input regions:\n"); struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE); puts("<BLOCKQUOTE><PRE>\n"); while (lineFileNext(errFile, &line, &lineSize)) puts(line); lineFileClose(&errFile); puts("</PRE></BLOCKQUOTE>\n"); } if (sameString(dataFormat, POSITION_FORMAT) && multiple) { puts("<BLOCKQUOTE><PRE>\n"); puts("Note: multiple checkbox ignored since it is not supported for position format."); puts("</PRE></BLOCKQUOTE>\n"); } carefulClose(&unmapped); } webDataFormats(); webDownloads(); cartWebEnd(); }
static struct bed *intersectOnRegion( struct sqlConnection *conn, /* Open connection to database. */ struct region *region, /* Region to work inside */ char *table1, /* Table input list is from. */ struct bed *bedList1, /* List before intersection, should be * all within region. */ struct lm *lm, /* Local memory pool. */ int *retFieldCount) /* Field count. */ /* Intersect bed list, consulting CGI vars to figure out * with what table and how. Return intersected result, * which is independent from input. This potentially will * chew up bedList1. */ { /* Grab parameters for intersection from cart. */ double moreThresh = cartCgiUsualDouble(cart, hgtaMoreThreshold, 0); double lessThresh = cartCgiUsualDouble(cart, hgtaLessThreshold, 100); boolean invTable = cartCgiUsualBoolean(cart, hgtaInvertTable, FALSE); char *op = intersectOp(); /* --- TODO MIKE - replace bedList2, bits2 with baseMask stuff. */ /* Load up intersecting bedList2 (to intersect with) */ int chromSize = hChromSize(database, region->chrom); boolean isBpWise = (sameString("and", op) || sameString("or", op)); Bits *bits2 = bitsForIntersectingTable(conn, region, chromSize, isBpWise); /* Set up some other local vars. */ struct hTableInfo *hti1 = getHti(database, table1, conn); struct bed *intersectedBedList = NULL; /* Produce intersectedBedList. */ if (isBpWise) { /* --- TODO MIKE - replace, bits1 with baseMask stuff. */ /* Base-pair-wise operation: get bitmap for primary table too */ Bits *bits1 = bitAlloc(chromSize+8); boolean hasBlocks = hti1->hasBlocks; if (retFieldCount != NULL && (*retFieldCount < 12)) hasBlocks = FALSE; bedOrBits(bits1, chromSize, bedList1, hasBlocks, 0); /* invert inputs if necessary */ if (invTable) bitNot(bits1, chromSize); /* do the intersection/union */ if (sameString("and", op)) bitAnd(bits1, bits2, chromSize); else bitOr(bits1, bits2, chromSize); /* clip to region if necessary: */ if (region->start > 0) bitClearRange(bits1, 0, region->start); if (region->end < chromSize) bitClearRange(bits1, region->end, (chromSize - region->end)); /* translate back to bed */ intersectedBedList = bitsToBed4List(bits1, chromSize, region->chrom, 1, region->start, region->end, lm); if (retFieldCount != NULL) *retFieldCount = 4; bitFree(&bits1); } else intersectedBedList = filterBedByOverlap(bedList1, hti1->hasBlocks, op, moreThresh, lessThresh, bits2, chromSize); bitFree(&bits2); return intersectedBedList; }
struct bbiInterval *intersectedFilteredBbiIntervalsOnRegion(struct sqlConnection *conn, struct bbiFile *bwf, struct region *region, enum wigCompare filterCmp, double filterLl, double filterUl, struct lm *lm) /* Get list of bbiIntervals (more-or-less bedGraph things from bigWig) out of bigWig file * and if necessary apply filter and intersection. Return list which is allocated in lm. */ { char *chrom = region->chrom; int chromSize = hChromSize(database, chrom); struct bbiInterval *iv, *ivList = bigWigIntervalQuery(bwf, chrom, region->start, region->end, lm); /* Run filter if necessary */ if (filterCmp != wigNoOp_e) { struct bbiInterval *next, *newList = NULL; for (iv = ivList; iv != NULL; iv = next) { next = iv->next; if (wigCompareValFilter(iv->val, filterCmp, filterLl, filterUl)) { slAddHead(&newList, iv); } } slReverse(&newList); ivList = newList; } /* Run intersection if necessary */ if (anyIntersection()) { boolean isBpWise = intersectionIsBpWise(); Bits *bits2 = bitsForIntersectingTable(conn, region, chromSize, isBpWise); struct bbiInterval *next, *newList = NULL; double moreThresh = cartCgiUsualDouble(cart, hgtaMoreThreshold, 0)*0.01; double lessThresh = cartCgiUsualDouble(cart, hgtaLessThreshold, 100)*0.01; char *op = cartString(cart, hgtaIntersectOp); for (iv = ivList; iv != NULL; iv = next) { next = iv->next; int start = iv->start; int size = iv->end - start; int overlap = bitCountRange(bits2, start, size); if (isBpWise) { if (overlap == size) { slAddHead(&newList, iv); } else if (overlap > 0) { /* Here we have to break things up. */ double val = iv->val; struct bbiInterval *partIv = iv; // Reuse memory for first interval int s = iv->start, end = iv->end; for (;;) { s = bitFindSet(bits2, s, end); if (s >= end) break; int bitsSet = bitFindClear(bits2, s, end) - s; if (partIv == NULL) lmAllocVar(lm, partIv); partIv->start = s; partIv->end = s + bitsSet; partIv->val = val; slAddHead(&newList, partIv); partIv = NULL; s += bitsSet; if (s >= end) break; } } } else { double coverage = (double)overlap/size; if (intersectOverlapFilter(op, moreThresh, lessThresh, coverage)) { slAddHead(&newList, iv); } } } slReverse(&newList); ivList = newList; bitFree(&bits2); } return ivList; }