void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
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;
}
