static void simpleFillInSequence(char *seqDir, struct agpFrag *agpList,
DNA *dna, int dnaSize)
/* Fill in DNA array with sequences from simple clones. */
{
struct agpFrag *agp;
char underline = '_';
for (agp = agpList; agp != NULL; agp = agp->next)
{
char clone[128];
char path[512];
struct dnaSeq *seq;
int size;
strcpy(clone, agp->frag);
chopSuffixAt(clone,underline);
sprintf(path, "%s/%s.fa", seqDir, clone);
seq = faReadAllDna(path);
if (slCount(seq) != 1)
errAbort("Can only handle exactly one clone in %s.", path);
size = agp->fragEnd - agp->fragStart;
if (agp->strand[0] == '-')
reverseComplement(seq->dna + agp->fragStart, size);
memcpy(dna + agp->chromStart, seq->dna + agp->fragStart, size);
freeDnaSeq(&seq);
}
}
void writeSizeListToBedFile(FILE *File, struct sizeList *sList)
{
struct sizeList *sl=NULL;
char *name;
for ( sl = sList; sl != NULL; sl = sl->next)
{
if (endsWith(sl->name,"+") || endsWith(sl->name,"-"))
chopSuffixAt(sl->name, '_');
fprintf(File, "%s\t%d\t%d\t%s\n", sl->chrom, sl->chromStart, sl->chromEnd, sl->name);
}
}
static void saveProtFastaPath(struct brokenRefPepTbl* brpTbl,
struct brokenRefPep* brp,
char *mrnaAcc, char *mrnaFa)
/* save protein fasta file path; mangles mrnaFa string */
{
char protFa[PATH_LEN];
safef(brp->mrnaAcc, sizeof(brp->mrnaAcc), "%s", mrnaAcc);
chopSuffixAt(mrnaFa, '/');
safef(protFa, sizeof(protFa), "%s/pep.fa", mrnaFa);
// ignore result from hashStore()
(void) hashStore(brpTbl->protFaHash, protFa);
safef(brp->newFaPath, sizeof(brp->newFaPath), "%s", protFa);
brpTbl->numToRepair++;
}
static boolean drawGtexRBoxplot(char *geneName, struct tissueSampleVals *tsvList,
boolean doLogTransform, char *version, struct tempName *pngTn)
/* Draw a box-and-whiskers plot from GTEx sample data, using R boxplot */
{
/* Create R data frame. This is a tab-sep file, one row per sample,
* with columns for sample, tissue, rpkm */
struct tempName dfTn;
trashDirFile(&dfTn, "hgc", "gtexGene", ".df.txt");
FILE *f = fopen(dfTn.forCgi, "w");
if (f == NULL)
errAbort("can't create temp file %s", dfTn.forCgi);
fprintf(f, "sample\ttissue\trpkm\n");
struct tissueSampleVals *tsv;
int sampleId=1;
int i;
for (tsv = tsvList; tsv != NULL; tsv = tsv->next)
{
int count = tsv->count;
// remove trailing parenthesized phrases as not worth label length
chopSuffixAt(tsv->description, '(');
for (i=0; i<count; i++)
fprintf(f, "%d\t%s\t%0.3f\n", sampleId++, tsv->description, tsv->vals[i]);
}
fclose(f);
// Plot to PNG file
if (!pngTn)
return FALSE;
trashDirFile(pngTn, "hgc", "gtexGene", ".png");
char cmd[256];
/* Exec R in quiet mode, without reading/saving environment or workspace */
safef(cmd, sizeof(cmd), "Rscript --vanilla --slave hgcData/gtexBoxplot.R %s %s %s %s %s %s",
geneName, dfTn.forCgi, pngTn->forHtml,
doLogTransform ? "log=TRUE" : "log=FALSE", "order=alpha", version);
//NOTE: use "order=score" to order bargraph by median RPKM, descending
int ret = system(cmd);
if (ret == 0)
return TRUE;
return FALSE;
}
struct ctgInfo *ctgInfoLoadOne(struct lineFile *lf)
/* Load one line of ctgInfo from a whitespaces-separated file.
Dispose of this with ctgInfo(). */
{
struct ctgInfo *el = NULL;
char *row[5];
char *acc = NULL;
if (lineFileRow(lf, row))
{
AllocVar(el);
el->ctgName = cloneString(row[0]);
/* remove suffix to get accession */
acc = cloneString(row[0]);
chopSuffixAt(acc, '_');
el->acc = acc;
el->start = sqlUnsigned(row[3]);
el->end = sqlUnsigned(row[4]);
}
return el;
}
static void agpSangerUnfinished(char *agpFile, char *contigFasta, char *agpOut)
/* Fix agp to match unfinished contigs in fasta */
{
struct lineFile *lf = lineFileOpen(agpFile, TRUE);
char *line, *words[16];
int lineSize, wordCount;
unsigned lastPos = 0;
struct agpFrag *agp;
struct agpGap *gap;
FILE *f;
char *lastObj = NULL;
f = mustOpen(agpOut, "w");
char *newChrom = NULL;
struct hash *hash = hashFasta(contigFasta);
verbose(2,"#\tprocessing AGP file: %s\n", agpFile);
while (lineFileNext(lf, &line, &lineSize))
{
if (line[0] == 0 || line[0] == '#' || line[0] == '\n')
continue;
//verbose(2,"#\tline: %d\n", lf->lineIx);
wordCount = chopLine(line, words);
if (wordCount < 5)
errAbort("Bad line %d of %s: need at least 5 words, got %d\n",
lf->lineIx, lf->fileName, wordCount);
if (!lastObj || !sameString(words[0],lastObj))
{
freez(&newChrom);
newChrom = cloneString(words[0]);
lastPos = 0;
}
if (words[4][0] != 'N')
{
lineFileExpectAtLeast(lf, 9, wordCount);
agp = agpFragLoad(words);
/* agp is 1-based but agp loaders do not adjust for 0-based: */
agp->chromStart -= 1;
agp->fragStart -= 1;
if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart)
errAbort("Sizes don't match in %s and %s line %d of %s\n",
agp->chrom, agp->frag, lf->lineIx, lf->fileName);
char *root = cloneString(agp->frag);
chopSuffixAt(root, '.');
struct hashEl *e, *elist = hashLookup(hash, root);
for (e = elist; e; e = hashLookupNext(e))
{
struct unfinishedContig *u = e->val;
if ((u->fragStart <= agp->fragStart) && (u->fragEnd >= agp->fragEnd))
{
agp->frag = cloneString(u->frag);
agp->fragEnd -= u->fragStart;
agp->fragStart -= u->fragStart;
}
}
freeMem(root);
}
else
{
lineFileExpectAtLeast(lf, 8, wordCount);
gap = agpGapLoad(words);
/* to be consistent with agpFrag */
gap->chromStart -= 1;
agp = (struct agpFrag*)gap;
}
if (agp->chromStart != lastPos)
errAbort("Start doesn't match previous end line %d of %s\n"
"agp->chromStart: %u\n"
"agp->chromEnd: %u\n"
"lastPos: %u\n"
,lf->lineIx, lf->fileName
,agp->chromStart
,agp->chromEnd
,lastPos
);
lastPos = agp->chromEnd;
freez(&lastObj);
lastObj = cloneString(words[0]); /* not agp->chrom which may be modified already */
if (words[4][0] != 'N')
{
/* agpFragOutput assumes 0-based-half-open, but writes 1-based for agp */
agpFragOutput(agp, f, '\t', '\n');
agpFragFree(&agp);
}
else
{
/* restore back to 1-based for agp
* because agpGapOutput doesn't compensate */
gap->chromStart += 1;
agpGapOutput(gap, f, '\t', '\n');
agpGapFree(&gap);
}
}
carefulClose(&f);
}
void configMultiRegionPage()
/* Do multi-region config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
int vis = -2;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<BR>\n");
hTableStart();
virtModeType = cartUsualString(cart, "virtModeType", virtModeType);
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Exit multi-region mode");
hPrintf("</TD></TR>\n");
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database)) // no db conn for assembly hubs
conn = hAllocConn(database);
// Do we have a gene table for exonMostly?
findBestEMGeneTable(trackList);
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show exons using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
/* obsolete
if (conn && sqlTableExists(conn,"knownCanonical"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show gene regions genome-wide.");
hPrintf("</TD></TR>\n");
}
*/
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Enter Custom regions as BED, or a URL to them:<br>");
multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl);
struct dyString *dyMultiRegionsBedInput = dyStringNew(256);
if (strstr(multiRegionsBedUrl,"://"))
{
dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl);
}
else
{
if (fileExists(multiRegionsBedUrl))
{
struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE);
char *line;
int lineSize;
while (lineFileNext(lf, &line, &lineSize))
{
dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line);
}
lineFileClose(&lf);
}
}
hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>",
dyMultiRegionsBedInput->string);
hPrintf("</TD></TR>\n");
/* The AllChroms option will be released in future
if (emGeneTable && sqlTableExists(conn, emGeneTable))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel);
char *trans = cartUsualString(cart, "singleTransId", singleTransId);
char sql[1024];
sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans);
char *result = sqlQuickString(conn, sql);
if (!result)
{
sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable);
trans = sqlQuickString(conn, sql);
}
hTextVar("singleTransId", trans, 20);
hPrintf("</TD></TR>\n");
}
*/
if (conn)
{
boolean altLocExists = sqlTableExists(conn, "altLocations");
boolean fixLocExists = sqlTableExists(conn, "fixLocations");
if (altLocExists || fixLocExists)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleAltHaplo",
sameWord("singleAltHaplo", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show one alternate haplotype");
if (fixLocExists)
hPrintf(" or fix patch");
hPrintf(", placed on its chromosome, using ID: ");
char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId);
char *foundHaplo = NULL;
char sql[1024];
if (altLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo && fixLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo)
{
if (altLocExists)
sqlSafef(sql, sizeof sql, "select name from altLocations limit 1");
else
sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1");
haplo = sqlQuickString(conn, sql);
chopSuffixAt(haplo, ':');
}
hTextVar("singleAltHaploId", haplo, 60);
hPrintf("</TD></TR>\n");
}
}
/* disable demo for now
if (sameString(database,"hg19") || sameString(database, "hg38"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo2 multiple ");
hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3);
hPrintf(" windows on one chrom chr21 def posn, window size ");
hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3);
hPrintf(" and step size ");
hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3);
hPrintf(" exon-like");
hPrintf("</TD></TR>\n");
*/
/* The AllChroms option will be released in future
if (conn) // requires chromInfo from database.
{ // TODO allow it to use assembly hubs via trackHubAllChromInfo() ?
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType));
hPrintf("</TD><TD>");
hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks.");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2.");
hPrintf("</TD></TR>\n");
*/
hTableEnd();
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>");
hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE));
hPrintf("</TD><TD>");
hPrintf("Highlight alternating regions in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px;width:650px \">\n");
hPrintf("<TR><TD>");
cgiMakeButton("topSubmit", "submit");
hPrintf("</TD><TD align=right>");
hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hFreeConn(&conn);
cgiDown(0.9);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
static void agpMergeChromScaf(char *agpFile, char *agpOut, boolean filtering)
/* Create a combined agp file from the chrom.agp and scaffold.agp,
* merging in only scaffolds from scaffold.agp
* that are not already in chroms. */
{
struct lineFile *lf = lineFileOpen(agpFile, TRUE);
char *line, *words[16];
int lineSize, wordCount;
unsigned lastPos = 0;
struct agpFrag *agp;
struct agpGap *gap;
FILE *f;
char *lastObj = NULL;
f = mustOpen(agpOut, filtering ? "a" : "w");
char *newChrom = NULL;
static struct hash *hash = NULL;
boolean skipping = FALSE;
if (!hash)
hash = hashNew(0);
verbose(2,"#\tprocessing AGP file: %s\n", agpFile);
while (lineFileNext(lf, &line, &lineSize))
{
if (line[0] == 0 || line[0] == '#' || line[0] == '\n')
continue;
//verbose(2,"#\tline: %d\n", lf->lineIx);
wordCount = chopLine(line, words);
if (wordCount < 5)
errAbort("Bad line %d of %s: need at least 5 words, got %d\n",
lf->lineIx, lf->fileName, wordCount);
if (!lastObj || !sameString(words[0],lastObj))
{
freez(&newChrom);
newChrom = cloneString(words[0]);
lastPos = 0;
}
skipping = FALSE;
if (filtering)
{
if (hashLookup(hash, words[0]))
skipping = TRUE;
}
if (words[4][0] != 'N')
{
lineFileExpectAtLeast(lf, 9, wordCount);
agp = agpFragLoad(words);
/* agp is 1-based but agp loaders do not adjust for 0-based: */
agp->chromStart -= 1;
agp->fragStart -= 1;
if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart)
errAbort("Sizes don't match in %s and %s line %d of %s\n",
agp->chrom, agp->frag, lf->lineIx, lf->fileName);
if (!filtering)
{
char *root = cloneString(agp->frag);
chopSuffixAt(root, '.');
hashStore(hash, root);
freeMem(root);
}
}
else
{
lineFileExpectAtLeast(lf, 8, wordCount);
gap = agpGapLoad(words);
/* to be consistent with agpFrag */
gap->chromStart -= 1;
agp = (struct agpFrag*)gap;
}
if (agp->chromStart != lastPos)
errAbort("Start doesn't match previous end line %d of %s\n"
"agp->chromStart: %u\n"
"agp->chromEnd: %u\n"
"lastPos: %u\n"
,lf->lineIx, lf->fileName
,agp->chromStart
,agp->chromEnd
,lastPos
);
lastPos = agp->chromEnd;
freez(&lastObj);
lastObj = cloneString(words[0]); /* not agp->chrom which may be modified already */
if (words[4][0] != 'N')
{
/* agpFragOutput assumes 0-based-half-open, but writes 1-based for agp */
if (!skipping)
agpFragOutput(agp, f, '\t', '\n');
agpFragFree(&agp);
}
else
{
/* restore back to 1-based for agp
* because agpGapOutput doesn't compensate */
gap->chromStart += 1;
if (!skipping)
agpGapOutput(gap, f, '\t', '\n');
agpGapFree(&gap);
}
}
carefulClose(&f);
}
static void clusterClone(int argc, char *argv[])
{
int i;
for (i=1; i < argc; ++i)
{
struct lineFile *lf;
struct psl *psl;
unsigned tSize;
char *prevAccPart = (char *)NULL;
char *prevAccName = (char *)NULL;
char *prevTargetName = (char *)NULL;
struct hashEl *el;
struct hash *chrHash = newHash(0);
struct hash *coordHash = newHash(0);
struct coordEl *coord;
struct coordEl **coordListPt = (struct coordEl **) NULL;
unsigned querySize = 0;
int partCount = 0;
int partsConsidered = 0;
verbose(2,"#\tprocess: %s\n", argv[i]);
lf=pslFileOpen(argv[i]);
while ((struct psl *)NULL != (psl = pslNext(lf)) )
{
char *accName = (char *)NULL;
char *targetName = (char *)NULL;
int chrCount = 0;
double percentCoverage;
accName = cloneString(psl->qName);
if ((char *)NULL == prevAccPart)
{
prevAccPart = cloneString(psl->qName); /* first time */
querySize = psl->qSize;
++partsConsidered;
}
chopSuffixAt(accName,'_');
if ((char *)NULL == prevAccName)
prevAccName = cloneString(accName); /* first time */
if ((char *)NULL == prevTargetName)
prevTargetName = cloneString(psl->tName); /* first time */
/* encountered a new accession name, process the one we
* were working on
*/
if (differentWord(accName, prevAccName))
{
if (partCount > 0)
processResult(chrHash, coordHash, prevAccName, querySize,
partsConsidered);
else
verbose(1,"# ERROR %s %s - no coordinates found in %d parts considered\n",
prevTargetName, prevAccName, partsConsidered);
freeMem(prevAccName);
prevAccName = cloneString(accName);
freeHash(&chrHash);
freeHash(&coordHash);
chrHash = newHash(0);
coordHash = newHash(0);
querySize = 0;
partCount = 0;
partsConsidered = 0;
}
tSize = psl->tEnd - psl->tStart;
percentCoverage = 100.0*((double)(tSize+1)/(psl->qSize + 1));
if (differentWord(psl->qName, prevAccPart))
{
++partsConsidered;
querySize += psl->qSize;
freeMem(prevAccPart);
prevAccPart = cloneString(psl->qName);
}
targetName = cloneString(psl->tName);
if (differentWord(targetName, prevTargetName))
{
freeMem(prevTargetName);
prevTargetName = cloneString(targetName);
}
/* keep a hash of chrom names encountered */
el = hashLookup(chrHash, targetName);
if (el == NULL)
{
if (percentCoverage > minCover)
{
hashAddInt(chrHash, targetName, 1);
chrCount = 1;
}
else
{
hashAddInt(chrHash, targetName, 0);
chrCount = 0;
}
}
else
{
if (percentCoverage > minCover)
{
chrCount = ptToInt(el->val) + 1;
el->val=intToPt(chrCount);
}
}
AllocVar(coord);
coord->start = psl->tStart;
coord->end = psl->tEnd;
coord->qSize = psl->qSize;
coord->strand = sameWord(psl->strand,"+") ? 1 : 0;
/* when coverage is sufficient */
if (percentCoverage > minCover)
{
++partCount;
coord->name = cloneString(psl->qName);
/* for each chrom name, accumulate a list of coordinates */
el = hashLookup(coordHash, targetName);
if (el == NULL)
{
AllocVar(coordListPt);
hashAdd(coordHash, targetName, coordListPt);
}
else
{
coordListPt = el->val;
}
slAddHead(coordListPt,coord);
verbose(2,"# %s\t%u\t%u\t%u\t%.4f\t%d %s:%d-%d %s\n",
psl->qName, psl->qSize, tSize, tSize - psl->qSize,
percentCoverage, chrCount, psl->tName, psl->tStart, psl->tEnd,
psl->strand);
}
else
{
verbose(3,"# %s\t%u\t%u\t%u\t%.4f\t%d %s:%d-%d %s\n",
psl->qName, psl->qSize, tSize, tSize - psl->qSize,
percentCoverage, chrCount, psl->tName, psl->tStart, psl->tEnd,
psl->strand);
}
freeMem(accName);
freeMem(targetName);
pslFree(&psl);
}
if (partCount > 0)
processResult(chrHash, coordHash, prevAccName, querySize,
partsConsidered);
else
verbose(1,"# ERROR %s %s - no coordinates found\n",
prevTargetName, prevAccName);
freeMem(prevAccName);
freeHash(&chrHash);
freeHash(&coordHash);
lineFileClose(&lf);
}
} /* static void clusterClone() */
