bool Record::intersects(const Record *record,
bool wantSameStrand, bool wantDiffStrand, float overlapFraction, bool reciprocal) const
{
//must be on same chromosome
if (!sameChrom(record)) {
return false;
}
return sameChromIntersects(record, wantSameStrand, wantDiffStrand, overlapFraction, reciprocal);
}
bool Record::operator > (const Record &other) const {
if (!sameChrom(&other)) {
return chromAfter(&other);
}
if (_startPos != other._startPos) {
return _startPos > other._startPos;
}
if (_endPos != other._endPos) {
return _endPos > other._endPos;
}
return false;
}
bool Record::lessThan(const Record *other) const
{
if (!sameChrom(other)) {
return chromBefore(other);
}
if (_startPos != other->_startPos) {
return _startPos < other->_startPos;
}
if (_endPos != other->_endPos) {
return _endPos < other->_endPos;
}
return false;
}
bool Record::operator < (const Record &other) const
{
if (!sameChrom(&other)) {
return chromBefore(&other);
}
if (_startPos != other._startPos) {
return _startPos < other._startPos;
}
if (_endPos != other._endPos) {
return _endPos < other._endPos;
}
return false;
}
bool Record::greaterThan(const Record *other) const
{
if (!sameChrom(other)) {
return chromAfter(other);
}
if (_startPos != other->_startPos) {
return _startPos > other->_startPos;
}
if (_endPos != other->_endPos) {
return _endPos > other->_endPos;
}
return false;
}
bool Record::intersects(const Record *record,
bool sameStrand,
bool diffStrand,
float overlapFractionA,
float overlapFractionB,
bool reciprocalFraction,
bool eitherFraction) const
{
//must be on same chromosome
if (!sameChrom(record)) {
return false;
}
return sameChromIntersects(record,
sameStrand, diffStrand,
overlapFractionA, overlapFractionB,
reciprocalFraction, eitherFraction);
}
bool Record::after(const Record *other) const
{
return (sameChrom(other) && _startPos >= other->_endPos);
}
void cdnaOnOoJobs(char *ooDir, char *conDir, int cdnaCount, char *cdnaTypes[])
/* cdnaOnOoJobs - make condor submission file for EST and mRNA alignments on draft assembly. */
{
char chromDir[512];
char chromFile[512];
char conFile[512];
char shFile[512];
char conPslDir[512];
char conOutDir[512];
char conErrDir[512];
char conLogDir[512];
char conInDir[512];
struct fileInfo *cfaList, *cfa;
struct fileInfo *chromList, *chromEl;
static char lastChromName[64] = "9X8Y"; /* Something uniq. */
boolean lastDoFull = FALSE;
FILE *con, *sh;
int i;
/* Set up basic directory structure in output dir. */
makeDir(conDir);
sprintf(conPslDir, "%s/psl", conDir);
makeDir(conPslDir);
sprintf(conOutDir, "%s/out", conDir);
makeDir(conOutDir);
sprintf(conLogDir, "%s/log", conDir);
makeDir(conLogDir);
sprintf(conErrDir, "%s/err", conDir);
makeDir(conErrDir);
sprintf(conInDir, "%s/in", conDir);
makeDir(conInDir);
/* Create list files for mrna and est. */
for (i=0; i<cdnaCount; i++)
{
char fileName[512];
sprintf(fileName, "/var/tmp/hg/h/mrna/%s.fa", cdnaTypes[i]);
makeSimpleIn(conInDir, cdnaTypes[i], fileName);
}
/* Create condor submission file and write header. */
sprintf(conFile, "%s/all.con", conDir);
con = mustOpen(conFile, "w");
fprintf(con, "#File created by cdnaOnOoJobs %s %s\n\n", ooDir, conDir);
fprintf(con,
"universe = vanilla\n"
"notification = error\n"
"requirements = memory > 250\n"
"executable = /cse/guests/kent/bin/i386/psLayout\n"
"initialdir = %s\n"
"\n"
, conDir);
/* Create shell script to finish job. */
sprintf(shFile, "%s/finish.sh", conDir);
sh = mustOpen(shFile, "w");
/* Loop through each chromosome directory. */
chromList = listDirX(ooDir, "*", FALSE);
for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next)
{
int len = strlen(chromEl->name);
if (chromEl->isDir && len <= 2)
{
sprintf(chromDir, "%s/%s", ooDir, chromEl->name);
cfaList = listDirX(chromDir, "chr*.fa", FALSE);
slSort(&cfaList, cmpFileInfoUnderbar);
/* Get list of assembled chromosomes in dir. */
for (cfa = cfaList; cfa != NULL; cfa = cfa->next)
{
/* See if is _random version of previous chromosome, in which
* case we follow the lead of last time. */
printf("%s size %d\n", cfa->name, cfa->size);
sprintf(chromFile, "%s/%s", chromDir, cfa->name);
if (sameChrom(lastChromName, cfa->name))
{
if (lastDoFull)
{
for (i=0; i<cdnaCount; ++i)
doFullJob(con, chromFile, lastChromName, conDir, conPslDir,
conOutDir, conLogDir, conErrDir, conInDir, cdnaTypes[i]);
}
}
else
{
strcpy(lastChromName, cfa->name);
chopSuffix(lastChromName);
if (cfa->size < 60000000)
{
lastDoFull = TRUE;
for (i=0; i<cdnaCount; ++i)
doFullJob(con, chromFile, lastChromName, conDir, conPslDir, conOutDir,
conLogDir, conErrDir, conInDir, cdnaTypes[i]);
}
else
{
lastDoFull = FALSE;
for (i=0; i<cdnaCount; ++i)
doPieceJob(con, sh, ooDir, lastChromName+3, cdnaTypes[i],
conDir, conPslDir, conOutDir, conLogDir, conErrDir, conInDir);
}
}
}
}
}
}
