void writeAliasTable(FILE *alias)
/* print out tabbed file for loading into the alias table, bacCloneAlias */
{
struct hashEl *aliasList = NULL, *aliasEl = NULL;
struct hashEl *bacList = NULL, *bacEl = NULL;
struct alias *al = NULL;
struct bac *bac = NULL;
char *name = NULL;
int i, j;
aliasList = hashElListHash(aliasHash);
bacList = hashElListHash(bacHash);
if (aliasList != NULL)
{
/* walk through list of hash elements */
for (aliasEl = aliasList; aliasEl != NULL; aliasEl = aliasEl->next)
{
al = (struct alias *)aliasEl->val;
name = cloneString(aliasEl->name);
/* print out row for Sanger STS name and each alias */
for (i = 0; i < NUMALIASES && (al->aliases[i] != NULL); i++)
{
fprintf(alias, "%s\t%s\n", al->aliases[i], al->sangerName);
}
fflush(alias);
}
}
else
errAbort("The hash of BAC clones aliases is empty or there was an error retrieving the list of entries in the hash\n");
/* those BAC clones without an entry in the alias hash have no sangerName */
/* so do not print to this table */
hashElFreeList(&aliasList);
hashElFreeList(&bacList);
}
void printCounts(struct hash *counts)
{
struct hashEl *el, *els = hashElListHash(counts);
slSort(&els, hashElCmp);
for (el = els; el != NULL; el = el->next)
printf(" %s %d\n", el->name, ptToInt(el->val));
}
struct bed* metaBig_chopGenome(struct metaBig* mb, int size)
/* return a bed of regularly-sized intervals (given) from the chromSizeHash */
{
struct hashEl* list = hashElListHash(mb->chromSizeHash);
struct hashEl* el;
struct bed* bed_list = NULL;
for (el = list; el != NULL; el = el->next) {
char* chrom = el->name;
int chromSize = ptToInt(el->val);
int i;
for (i = 0; i < chromSize; i += size) {
struct bed* newbed;
AllocVar(newbed);
newbed->chrom = cloneString(chrom);
newbed->chromStart = i;
if ((i + size) > chromSize)
newbed->chromEnd = chromSize;
else
newbed->chromEnd = i + size;
newbed->name = cloneString(".");
slAddHead(&bed_list, newbed);
}
}
if (mb->sections)
subset_with_sections(mb, &bed_list);
slReverse(&bed_list);
return bed_list;
}
struct hashEl *peakClusterMakerChromList(struct peakClusterMaker *maker)
/* Return list of chromosomes. In hashEl format where the hashEl val is
* a rangeTree filled with items. */
{
struct hashEl *chromList = hashElListHash(maker->chromHash);
slSort(&chromList, cmpChromEls);
return chromList;
}
void edwBamToWig(char *input, char *output)
/* edwBamToWig - Convert a bam file to a wig file by measuring depth of coverage, optionally adjusting hit size to average for library.. */
{
FILE *f = mustOpen(output, "w");
/* Open file and get header for it. */
samfile_t *sf = samopen(input, "rb", NULL);
if (sf == NULL)
errnoAbort("Couldn't open %s.\n", input);
bam_header_t *head = sf->header;
if (head == NULL)
errAbort("Aborting ... Bad BAM header in file: %s", input);
/* Scan through input populating genome range trees */
struct genomeRangeTree *grt = genomeRangeTreeNew();
bam1_t one = {};
for (;;)
{
/* Read next record. */
if (bam_read1(sf->x.bam, &one) < 0)
break;
if (one.core.tid >= 0 && one.core.n_cigar > 0)
{
char *chrom = head->target_name[one.core.tid];
int start = one.core.pos;
int end = start + one.core.l_qseq;
if (one.core.flag & BAM_FREVERSE)
{
start -= clPad;
}
else
{
end += clPad;
}
struct rbTree *rt = genomeRangeTreeFindOrAddRangeTree(grt,chrom);
rangeTreeAddToCoverageDepth(rt, start, end);
}
}
/* Convert genome range tree into output wig */
/* Get list of chromosomes. */
struct hashEl *hel, *helList = hashElListHash(grt->hash);
for (hel = helList; hel != NULL; hel = hel->next)
{
char *chrom = hel->name;
struct rbTree *rt = hel->val;
struct range *range, *rangeList = rangeTreeList(rt);
for (range = rangeList; range != NULL; range = range->next)
{
fprintf(f, "%s\t%d\t%d\t%d\n", chrom, range->start, range->end, ptToInt(range->val));
}
}
carefulClose(&f);
}
static struct hash* splitByPrefix(struct gbConf *conf)
/* split by prefix in to has of prefixElems */
{
struct hash *prefixMap = hashNew(18);
struct hashEl *elems = hashElListHash(conf->hash);
struct hashEl *confEl;
while ((confEl = slPopHead(&elems)) != NULL)
addByPrefix(prefixMap, confEl);
return prefixMap;
}
/* one iteration of convolution
*
* input is a probability histogram with N bins
* bins are numbered 0 through N-1
* output is a probability histogram with (N*2)-1 bins
*
* The value to calculate in an output bin is a sum
* of the probabilities from the input bins that contribute to that
* output bin. Specifically:
*
* output[0] = input[0] * input[0]
* output[1] = (input[0] * input[1]) +
* (input[1] * input[0])
* output[2] = (input[0] * input[2]) +
* (input[1] * input[1]) +
* (input[2] * input[0])
* output[3] = (input[0] * input[3]) +
* (input[1] * input[2]) +
* (input[2] * input[1]) +
* (input[3] * input[0])
* output[4] = (input[0] * input[4]) +
* (input[1] * input[3]) +
* (input[2] * input[2]) +
* (input[3] * input[1]) +
* (input[4] * input[0])
* the pattern here is that the bin numbers from the input are
* summed together to get the bin number of the output. The
* probabilities from those bins used from the input in each
* individual sum are multiplied together, and all those resulting
* multiplies are added together for the resulting output.
*
* A double for() loop would do the above calculation:
* for (i = 0; i < N; ++i) {
* for (j = 0; j < N; ++j) {
* output[i+j] += input[i] * input[j];
* }
* }
*/
static int iteration(struct hash *input, struct hash *output)
{
struct hashEl *el, *elList;
int median = 0;
double maxLog = -1000000.0;
/* This outside loop is like (i = 0; i < N; ++i) */
elList = hashElListHash(input);
for (el = elList; el != NULL; el = el->next)
{
struct histoGram *hg0; /* a hash element */
struct hashEl *elInput;
int bin0;
/* This inside loop is like (j = 0; j < N; ++j) */
hg0 = el->val;
bin0 = hg0->bin;
for (elInput = elList; elInput != NULL; elInput = elInput->next)
{
struct histoGram *hg1; /* a hash element */
int bin1;
char binName[128];
struct hashEl *el;
struct histoGram *hgNew;
hg1 = elInput->val;
bin1 = hg1->bin;
/* output bin name is (i+j) == (bin0+bin1) */
snprintf(binName, sizeof(binName), "%d", bin0+bin1);
el = hashLookup(output, binName);
/* start new output bin if it does not yet exist */
if (el == NULL) {
AllocVar(hgNew);
hgNew->bin = bin0+bin1;
hgNew->prob = hg0->prob * hg1->prob;
hgNew->log_2 = hg0->log_2 + hg1->log_2;
hashAdd(output, binName, hgNew);
} else { /* Add to existing output bin the new inputs */
hgNew = el->val;
hgNew->log_2 =
addLogProbabilities(hgNew->log_2, (hg0->log_2+hg1->log_2));
hgNew->prob = pow(2.0,hgNew->log_2);
}
/* Keep track of the resulting output median */
if (hgNew->log_2 > maxLog)
{
maxLog = hgNew->log_2;
median = hgNew->bin;
}
}
}
hashElFreeList(&elList);
return median;
} /* iteration() */
void writeHashToFile(struct hash *countHash, char *outputFile)
/* Make an slPair list out of a hashEl list, sort it, output it. */
{
FILE *f = mustOpen(outputFile, "w");
struct hashEl *el, *list = hashElListHash(countHash);
slNameSort((struct slName **)&list);
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s\t%d\n", el->name, ptToInt(el->val));
carefulClose(&f);
hashElFreeList(&list);
}
void printHash(char *label, struct hash *hash)
/* Print out keys in hash alphabetically. */
{
struct hashEl *list, *el;
list = hashElListHash(hash);
slSort(&list, hashElCmp);
printf("%s:\n", label);
for (el = list; el != NULL; el = el->next)
printf(" %s\n", el->name);
hashElFreeList(&list);
}
void doEnrichmentsFromBed3Sample(struct bed3 *sampleList,
struct sqlConnection *conn,
struct cdwFile *ef, struct cdwValidFile *vf,
struct cdwAssembly *assembly, struct target *targetList)
/* Given a bed3 list, calculate enrichments for targets */
{
struct genomeRangeTree *sampleGrt = cdwMakeGrtFromBed3List(sampleList);
struct hashEl *chrom, *chromList = hashElListHash(sampleGrt->hash);
/* Iterate through each target - and in lockstep each associated grt to calculate unique overlap */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct genomeRangeTree *grt = target->grt;
long long uniqOverlapBases = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct rbTree *sampleTree = chrom->val;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
struct range *range, *rangeList = rangeTreeList(sampleTree);
for (range = rangeList; range != NULL; range = range->next)
{
/* Do unique base overlap counts (since using range trees both sides) */
int overlap = rangeTreeOverlapSize(targetTree, range->start, range->end);
uniqOverlapBases += overlap;
}
}
}
/* Figure out how much we overlap allowing same bases in genome
* to part of more than one overlap. */
long long overlapBases = 0;
struct bed3 *sample;
for (sample = sampleList; sample != NULL; sample = sample->next)
{
int overlap = genomeRangeTreeOverlapSize(grt,
sample->chrom, sample->chromStart, sample->chromEnd);
overlapBases += overlap;
}
/* Save to database. */
struct cdwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly,
target, overlapBases, uniqOverlapBases);
cdwQaEnrichSaveToDb(conn, enrich, "cdwQaEnrich", 128);
cdwQaEnrichFree(&enrich);
}
genomeRangeTreeFree(&sampleGrt);
hashElFreeList(&chromList);
}
static void printGbConf(FILE *fh, struct gbConf *conf)
/* Print contents of genbank.conf file for debugging purposes */
{
struct hashEl *confEls = hashElListHash(conf->hash);
struct hashEl *confEl;
slSort(&confEls, hashElCmp);
for (confEl = confEls; confEl != NULL; confEl = confEl->next)
fprintf(fh, "%s = %s\n", confEl->name, (char*)confEl->val);
hashElFreeList(&confEls);
}
struct slName *hashToList(struct hash *wordHash)
/* convert the hash back to a list. */
{
struct hashEl *elList = hashElListHash(wordHash);
struct slName *list = NULL;
struct hashEl *cur;
for (cur = elList; cur != NULL; cur = cur->next)
slNameAddHead(&list, cur->name);
slNameSort(&list);
hashElFreeList(&elList);
return list;
}
void weedLines(char *weedFile, char *file, char *output,
boolean invert, char *invertOutput)
/* weedLines - Selectively remove lines from file. */
{
struct hash *hash = hashWordsInFile(weedFile, 16);
struct hashEl *weedList = hashElListHash(hash);
verbose(2, "%d words in weed file %s\n", hash->elCount, weedFile);
struct lineFile *lf = lineFileOpen(file, TRUE);
char *line, *word;
FILE *f = mustOpen(output, "w");
FILE *fInvert = NULL;
boolean embedded = optionExists("embedded");
if (invertOutput != NULL)
fInvert = mustOpen(invertOutput, "w");
while (lineFileNext(lf, &line, NULL))
{
boolean doWeed = FALSE;
char *dupe = NULL;
if (embedded)
{
struct hashEl *hel;
for (hel = weedList; hel != NULL; hel = hel->next)
{
if (stringIn(hel->name, line))
doWeed = TRUE;
}
}
else
{
dupe = cloneString(line);
while ((word = nextWord(&line)) != NULL)
{
if (hashLookup(hash, word))
doWeed = TRUE;
}
line = dupe;
}
if (invert)
doWeed = !doWeed;
if (!doWeed)
fprintf(f, "%s\n", line);
else
{
if (fInvert != NULL)
fprintf(fInvert, "%s\n", line);
}
freez(&dupe);
}
}
void edwSamRepeatAnalysis(char *inSam, char *outRa)
/* edwSamRepeatAnalysis - Analyze result of alignment vs. RepeatMasker type libraries.. */
{
/* Go through sam file, filling in hiLevelHash with count of each hi level repeat class we see. */
struct hash *hiLevelHash = hashNew(0);
samfile_t *sf = samopen(inSam, "r", NULL);
bam_header_t *bamHeader = sf->header;
bam1_t one;
ZeroVar(&one);
int err;
long long hit = 0, miss = 0;
while ((err = samread(sf, &one)) >= 0)
{
int32_t tid = one.core.tid;
if (tid < 0)
{
++miss;
continue;
}
++hit;
/* Parse out hiLevel classification from target, which is something like 7SLRNA#SINE/Alu
* from which we'd want to extract SINE. The '/' is not present in all input. */
char *target = bamHeader->target_name[tid];
char *hashPos = strchr(target, '#');
if (hashPos == NULL)
errAbort("# not found in target %s", target);
char *hiLevel = cloneString(hashPos + 1);
char *slashPos = strchr(hiLevel, '/');
if (slashPos != NULL)
*slashPos = 0;
hashIncInt(hiLevelHash, hiLevel);
}
samclose(sf);
/* Output some basic stats as well as contents of hash */
FILE *f = mustOpen(outRa, "w");
double invTotal = 1.0 / (hit + miss);
double mapRatio = (double)hit * invTotal;
struct hashEl *hel, *helList = hashElListHash(hiLevelHash);
slSort(&helList, hashElCmp);
for (hel = helList; hel != NULL; hel = hel->next)
{
double hitRatio = ptToInt(hel->val) * invTotal;
fprintf(f, "%s %g\n", hel->name, hitRatio);
}
fprintf(f, "total %g\n", mapRatio);
carefulClose(&f);
}
struct hash *minChromSizeKeeperHash(struct hash *sizeHash)
/* Return a hash full of binKeepers that match the input sizeHash,
* (which generally is the output of minChromSizeFromBeds). */
{
struct hashEl *el, *list = hashElListHash(sizeHash);
struct hash *keeperHash = hashNew(16);
for (el = list; el != NULL; el = el->next)
{
struct minChromSize *chrom = el->val;
struct binKeeper *bk = binKeeperNew(0, chrom->minSize);
hashAdd(keeperHash, chrom->chrom, bk);
}
hashElFreeList(&list);
return keeperHash;
}
char *hashToRaString(struct hash *hash)
/* Convert hash to string in ra format. */
{
struct hashEl *el, *list = hashElListHash(hash);
struct dyString *dy = dyStringNew(0);
slSort(&list, hashElCmp);
for (el = list; el != NULL; el = el->next)
{
dyStringAppend(dy, el->name);
dyStringAppendC(dy, ' ');
dyStringAppend(dy, el->val);
dyStringAppendC(dy, '\n');
}
hashElFreeList(&list);
return dyStringCannibalize(&dy);
}
static struct hash *joinerAllFields(struct joiner *joiner)
/* Get hash of all fields in database.table.field format.
* Similar to sqlAllFields(void) function in jksql.c, but different
* method of creating the list of databases to check.
*/
{
struct hash *fullHash = hashNew(18);
struct hashEl *db, *dbList = hashElListHash(joiner->databasesChecked);
for (db = dbList; db != NULL; db = db->next)
{
verbose(3, "joinerAllFields: extracting fields from database: '%s'\n",
db->name);
sqlAddDatabaseFields(db->name, fullHash);
}
slFreeList(&dbList);
return fullHash;
}
void userSettingsUseNamed(struct userSettings *us, char *setName)
/* Use named collection of settings. */
{
struct cart *cart = us->cart;
char *varName = settingsVarName(us->savePrefix, setName);
char *settings = cartOptionalString(cart, varName);
if (settings != NULL)
{
struct hash *hash = hashVarLine(settings, 1);
struct hashEl *list = hashElListHash(hash);
struct hashEl *el;
for (el = list; el != NULL; el = el->next)
cartSetString(cart, el->name, el->val);
slFreeList(&list);
hashFree(&hash);
}
freez(&varName);
}
static struct bed* sectionsFromChromSizes(struct hash* chromSizes)
/* return a list of bed3s used as sections using the whole chromosome sizes */
{
struct bed* bedList = NULL;
struct hashEl* list = hashElListHash(chromSizes);
struct hashEl* el;
for (el = list; el != NULL; el = el->next) {
struct bed* bed;
AllocVar(bed);
bed->chrom = cloneString(el->name);
bed->chromStart = 0;
bed->chromEnd = (unsigned)ptToInt(el->val);
slAddHead(&bedList, bed);
}
slReverse(&bedList);
hashElFreeList(&list);
return bedList;
}
static char *settingsFromHash(struct hash *hash)
/* Create settings string from settings hash. */
{
if (hash == NULL)
return cloneString("");
else
{
struct dyString *dy = dyStringNew(1024);
char *ret;
struct hashEl *el, *list = hashElListHash(hash);
slSort(&list, hashElCmp);
for (el = list; el != NULL; el = el->next)
dyStringPrintf(dy, "%s %s\n", el->name, (char *)el->val);
slFreeList(&list);
ret = cloneString(dy->string);
dyStringFree(&dy);
return ret;
}
}
void crTreeFileCreate(
struct crTreeItem *itemList, /* List of all items - sorted here and in underlying file. */
struct hash *chromHash, /* Hash of all chromosome names. */
bits32 blockSize, /* R tree block size - # of children for each node. 1024 is good. */
bits32 itemsPerSlot, /* Number of items to put in each index slot at lowest level.
* Typically either blockSize/2 or 1. */
bits64 endPosition, /* File offset after have read all items in file. */
char *fileName) /* Name of output file. */
/* Create a cr tree index of file. The itemList contains the position of each item in the
* chromosome and in the file being indexed. Both the file and the itemList must be sorted
* by chromosome (alphabetic), start (numerical), end (numerical).
* We recommend you run crTreeFileCreateInputCheck on the input parameters right before
* calling this if you have problems. */
{
/* We can't handle empty input... */
if (itemList == NULL)
errAbort("crTreeFileCreate can't handle empty itemList.");
/* Make array of pointers out of linked list. */
struct crTreeItem **itemArray;
bits32 itemCount = slCount(itemList);
AllocArray(itemArray, itemCount);
struct crTreeItem *item;
int itemIx;
for (itemIx=0, item=itemList; itemIx<itemCount; ++itemIx, item=item->next)
itemArray[itemIx] = item;
/* Make up chromosome array. */
int chromCount = chromHash->elCount;
char **chromArray;
AllocArray(chromArray, chromCount);
struct hashEl *el, *list = hashElListHash(chromHash);
bits32 chromIx;
for (el = list, chromIx=0; el != NULL; el = el->next, ++chromIx)
chromArray[chromIx] = el->name;
slFreeList(&list);
/* Call function to make index file. */
crTreeFileCreateLow(chromArray, chromCount, itemArray, sizeof(itemArray[0]), itemCount,
blockSize, itemsPerSlot, crTreeItemKey, crTreeItemOffset, itemList->fileOffset,
endPosition, fileName);
}
void joinerCheckTableCoverage(struct joiner *joiner, char *specificDb)
/* Check that all tables either are part of an identifier or
* are in the tablesIgnored statements. */
{
struct slName *miss, *missList = NULL;
struct hashEl *dbList, *db;
dbList = hashElListHash(joiner->databasesChecked);
for (db = dbList; db != NULL; db = db->next)
{
if (specificDb == NULL || sameString(db->name, specificDb))
{
struct sqlConnection *conn = sqlMayConnect(db->name);
if (conn == NULL)
warn("Error: database %s doesn't exist", db->name);
else
{
struct slName *table;
struct slName *tableList = sqlListTables(conn);
struct hash *hash = getCoveredTables(joiner, db->name, conn);
for (table = tableList; table != NULL; table = table->next)
{
if (!hashLookup(hash, table->name))
{
char fullName[256];
safef(fullName, sizeof(fullName), "%s.%s",
db->name, table->name);
miss = slNameNew(fullName);
slAddHead(&missList, miss);
}
else
verbose(2,"tableCovered: '%s'\n", table->name);
}
slFreeList(&tableList);
freeHash(&hash);
reportErrorList(&missList, "tables not in .joiner file");
}
sqlDisconnect(&conn);
}
}
slFreeList(&dbList);
}
void bwtool_lift(struct hash *options, char *favorites, char *regions, unsigned decimals,
enum wigOutType wot, char *bigfile, char *chainfile, char *outputfile)
/* bwtool_lift - main for lifting program */
{
struct hash *sizeHash = NULL;
struct hash *chainHash = readLiftOverMapChainHash(chainfile);
struct hash *gpbw = NULL;
char *size_file = hashFindVal(options, "sizes");
char *bad_file = hashFindVal(options, "unlifted");
if (size_file)
sizeHash = readCsizeHash(size_file);
else
sizeHash = qSizeHash(chainfile);
gpbw = genomePbw(sizeHash);
struct metaBig *mb = metaBigOpen_check(bigfile, regions);
char wigfile[512];
safef(wigfile, sizeof(wigfile), "%s.tmp.wig", outputfile);
FILE *out = mustOpen(wigfile, "w");
struct hashEl *elList = hashElListHash(gpbw);
struct hashEl *el;
verbose(2,"starting first pass\n");
do_pass1(mb, chainHash, gpbw);
verbose(2, "starting second pass\n");
do_pass2(mb, chainHash, gpbw);
verbose(2,"starting final pass\n");
do_final_pass(mb, chainHash, gpbw, bad_file);
slSort(&elList, pbwHashElCmp);
for (el = elList; el != NULL; el = el->next)
{
struct perBaseWig *pbw = (struct perBaseWig *)el->val;
perBaseWigOutputNASkip(pbw, out, wot, decimals, NULL, FALSE, FALSE);
}
hashElFreeList(&elList);
carefulClose(&out);
hashFreeWithVals(&chainHash, freeChainHashMap);
hashFreeWithVals(&gpbw, perBaseWigFree);
writeBw(wigfile, outputfile, sizeHash);
hashFree(&sizeHash);
remove(wigfile);
metaBigClose(&mb);
}
void agpNotInf(char *agpFile, char *infFile)
/* agpNotInf - List clones in .agp file not in .inf file. */
{
struct hash *agpHash = readAgp(agpFile);
struct hash *infHash = readInf(infFile);
struct hashEl *list, *el;
struct clone *agpClone, *infClone;
list = hashElListHash(agpHash);
uglyf("%d clones in agpHash\n", slCount(list));
for (el = list; el != NULL; el = el->next)
{
agpClone = el->val;
infClone = hashFindVal(infHash, agpClone->name);
if (infClone == NULL)
printf("%s missing\n", agpClone->version);
else if (!sameString(agpClone->version, infClone->version))
printf("%s updated from %s\n", agpClone->version, infClone->version);
}
hashElFreeList(&list);
}
void joinerCheckDependencies(struct joiner *joiner, char *specificDb)
/* Check time stamps on dependent tables. */
{
struct hashEl *db, *dbList = hashElListHash(joiner->databasesChecked);
for (db = dbList; db != NULL; db = db->next)
{
if (specificDb == NULL || sameString(specificDb, db->name))
{
struct sqlConnection *conn = sqlMayConnect(db->name);
if (conn != NULL) /* We've already warned on this NULL */
{
struct joinerDependency *dep;
for (dep = joiner->dependencyList; dep != NULL; dep = dep->next)
{
checkOneDependency(joiner, dep, conn, db->name);
}
sqlDisconnect(&conn);
}
}
}
slFreeList(&dbList);
}
struct hash *genomePbw(struct hash *qSizes)
/* make a parallel hash of pbws given the size hash, also keyed on chrom name */
{
struct hash *pbwHash = newHash(10);
struct hashEl *list = hashElListHash(qSizes);
struct hashEl *el;
const double na = NANUM;
int i;
for (el = list; el != NULL; el = el->next)
{
int size = ptToInt(el->val);
struct perBaseWig *pbw = alloc_perBaseWig(el->name, 0, size);
for (i = 0; i < pbw->len; i++)
pbw->data[i] = na;
pbw->name = cloneString(el->name);
pbw->strand[0] = '+';
pbw->strand[1] = '\0';
hashAdd(pbwHash, el->name, pbw);
}
hashElFreeList(&list);
return pbwHash;
}
static void checkIgnoreBalance(struct joiner *joiner)
/* Check that databases in fields are in the checked list.
* Check that there is no overlap between checked and ignored
* list. */
{
struct joinerSet *js;
struct joinerField *jf;
struct slName *db;
struct hashEl *ignoreList, *ignore;
/* Check that there is no overlap between databases ignored
* and databases checked. */
ignoreList = hashElListHash(joiner->databasesIgnored);
for (ignore=ignoreList; ignore != NULL; ignore = ignore->next)
{
if (hashLookup(joiner->databasesChecked, ignore->name))
errAbort("%s is in both databasesChecked and databasesIgnored",
ignore->name);
}
slFreeList(&ignoreList);
/* Check that all databases mentioned in fields are in
* databasesChecked. */
for (js = joiner->jsList; js != NULL; js = js->next)
{
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
for (db = jf->dbList; db != NULL; db = db->next)
{
if (!hashLookup(joiner->databasesChecked, db->name))
{
errAbort("database %s line %d of %s is not in databasesChecked",
db->name, jf->lineIx, joiner->fileName);
}
}
}
}
}
double calcBaseCoverage(struct hash *refHash, struct hash *geneHash)
/* Figure proportion refBases covered by genes. Both refHash and geneHash
* are keyed by chromosome and filled with genes. */
{
struct hashEl *chrom, *chromList = hashElListHash(refHash);
long totalRef = 0, totalOverlap = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
char *chromName = chrom->name;
struct binKeeper *refBk = chrom->val;
struct rbTree *refTree = bedBkToTree(refBk);
totalRef += rangeTreeTotalSize(refTree);
struct binKeeper *geneBk = hashFindVal(geneHash, chromName);
if (geneBk != NULL)
{
struct rbTree *geneTree = bedBkToTree(geneBk);
totalOverlap += rangeTreeRangeTreeOverlap(refTree, geneTree);
rangeTreeFree(&geneTree);
}
rangeTreeFree(&refTree);
}
return (double)totalOverlap / totalRef;
}
static void printDir(FILE *f, struct _pf_dir *dir, struct _pf_base *base,
struct hash *idHash)
/* Print out each key/val pair in dir. */
{
if (dir == NULL)
fprintf(f, "()");
else
{
if (idHash)
{
if (!reuseObject(f, idHash, dir))
{
struct hash *hash = dir->hash;
struct hashEl *hel, *helList = hashElListHash(hash);
struct _pf_base *base = dir->elType->base;
slSort(&helList, hashElCmp);
fprintf(f, "(");
for (hel = helList; hel != NULL; hel = hel->next)
{
fprintf(f, "'%s'@", hel->name);
if (base->needsCleanup)
_pf_printField(f, &hel->val, base, idHash);
else
_pf_printField(f, hel->val, base, idHash);
if (hel->next != NULL)
fprintf(f, ",");
}
hashElFreeList(&helList);
fprintf(f, ")");
}
}
else
{
fprintf(f, "<dir of %d>", dir->hash->elCount);
}
}
}
void nibTwoCacheFree(struct nibTwoCache **pNtc)
/* Free up resources associated with nibTwoCache. */
{
struct nibTwoCache *ntc = *pNtc;
if (ntc != NULL)
{
freez(&ntc->pathName);
if (ntc->isTwoBit)
twoBitClose(&ntc->tbf);
else
{
struct hashEl *el, *list = hashElListHash(ntc->nibHash);
struct nibInfo *nib;
for (el = list; el != NULL; el = el->next)
{
nib = el->val;
nibInfoFree(&nib);
}
hashElFreeList(&list);
hashFree(&ntc->nibHash);
}
freez(pNtc);
}
}