void pbwtDestroy (PBWT *p)
{
if (p->chrom) free (p->chrom) ;
if (p->sites) arrayDestroy (p->sites) ;
if (p->samples) arrayDestroy (p->samples) ;
if (p->yz) arrayDestroy (p->yz) ;
if (p->zz) arrayDestroy (p->zz) ;
if (p->aFstart) free (p->aFstart) ;
if (p->aFend) free (p->aFend) ;
if (p->aRstart) free (p->aRstart) ;
if (p->aRend) free (p->aRend) ;
free (p) ;
}
int main (int argc, char *argv[])
{
GfrEntry *currGE;
int count;
int countRemoved;
int i;
if (argc != 3) {
usage ("%s <offsetCutoff> <minNumUniqueReads>",argv[0]);
}
count = 0;
countRemoved = 0;
int offsetCutOff = atoi (argv[1]);
int minNumUniqueReads = atoi (argv[2]);
gfr_init ("-");
puts (gfr_writeHeader ());
while (currGE = gfr_nextEntry ()) {
Array starts = arrayCreate( 100, int);
for (i = 0; i < arrayMax( currGE->interReads ); i++) {
int currStart = arrp(currGE->interReads, i, GfrInterRead)->readStart1 + arrp(currGE->interReads, i, GfrInterRead)->readStart2;
array(starts, arrayMax(starts), int) = currStart;
}
arraySort( starts, (ARRAYORDERF) arrayIntcmp );
arrayUniq( starts, NULL, (ARRAYORDERF) arrayIntcmp ) ;
int numUniqeOffsets = arrayMax( starts );
arrayDestroy( starts );
if (arrayMax( currGE->readsTranscript1 ) != arrayMax( currGE->readsTranscript2 ) )
die( "The two ends have a different number of reads");
Texta reads = textCreate(arrayMax(currGE->readsTranscript1));
for (i = 0; i < arrayMax(currGE->readsTranscript1); i++) {
Stringa strA = stringCreate( strlen(textItem( currGE->readsTranscript1, i) ) * 2 + 1);
stringAppendf( strA, textItem( currGE->readsTranscript1,i));
stringAppendf( strA, textItem( currGE->readsTranscript2,i));
textAdd( reads, string(strA));
stringDestroy( strA );
}
textUniqKeepOrder( reads );
int numRemaining = arrayMax( reads );
textDestroy ( reads );
if (numRemaining <= minNumUniqueReads || numUniqeOffsets <= offsetCutOff) {
countRemoved++;
continue;
}
puts (gfr_writeGfrEntry (currGE));
count++;
}
gfr_deInit ();
warn("%s_PCRFilter: offset=%d minNumUniqueReads=%d",
argv[0],offsetCutOff, minNumUniqueReads);
warn("%s_numRemoved: %d",argv[0],countRemoved);
warn("%s_numGfrEntries: %d",argv[0],count);
return 0;
}
void hashDestroy (HASH hx)
{
TRUE_HASH *h = (TRUE_HASH*) hx ;
free (h->keys) ;
free (h->values) ;
arrayDestroy (h->freeList) ;
free (h) ;
++nDestroyed ;
}
int main (int argc, char *argv[])
{
GfrEntry *currGE;
int count;
int countRemoved;
int i, j;
int foundEST;
if (argc != 2) {
usage ("%s <EST.interval>",argv[0]);
}
intervalFind_addIntervalsToSearchSpace( argv[1], 0);
// beginFiltering
count = 0;
countRemoved = 0;
gfr_init ("-");
puts (gfr_writeHeader ());
while (currGE = gfr_nextEntry ()) { // reading the gfr
foundEST = 0;
if( strEqual( currGE->fusionType, "cis" ) ) {
if( ! strEqual( currGE->chromosomeTranscript1, currGE->chromosomeTranscript2 ) )
die("The two genes are not on the same chromosomes: %s - %s", currGE->chromosomeTranscript1, currGE->chromosomeTranscript2 );
int start1, end1, start2, end2;
findCoordinates( currGE, &start1, &end1, &start2, &end2 );
Array intervals1 = arrayCopy( intervalFind_getOverlappingIntervals( currGE->chromosomeTranscript1, start1, end1 ) );
Array intervals2 = intervalFind_getOverlappingIntervals( currGE->chromosomeTranscript2, start2, end2 );
for( i=0; i<arrayMax( intervals1 ); i++ ) {
Interval* currInterval1 = arru( intervals1, i, Interval* );
for( j=0; j<arrayMax ( intervals2 ); j++ ) {
Interval* currInterval2 = arru( intervals2, j, Interval* );
if( currInterval1==currInterval2 ) {
foundEST = 1;
i = arrayMax( intervals1 );
j = arrayMax( intervals2 );
}
}
}
arrayDestroy( intervals1 );
}
if( foundEST )
countRemoved++;
else {
puts (gfr_writeGfrEntry (currGE));
count++;
}
}
gfr_deInit ();
warn ("%s_EST_data: %s",argv[0], argv[1]);
warn ("%s_numRemoved: %d",argv[0], countRemoved);
warn ("%s_numGfrEntries: %d",argv[0],count);
return 0;
}
/**
* \file bgrQuantifier <annotation.interval>.
* \pre: it requires a BedGraph file from STDIN normalized by the number of mapped nucleotides
*/
int main( int argc, char* argv[] ) {
Array bgrs;
Array intervals;
Array entries;
int i, j, length;
double value;
if( argc < 2 ) {
usage("%s <annotation.interval>\n%s requires a BedGraph from STDIN", argv[0], argv[0]);
}
bgrs = arrayCreate( 1000, BedGraph );
bgrParser_initFromFile ( "-" );
bgrs = bgrParser_getAllEntries ();
bgrParser_deInit();
arraySort( bgrs, (ARRAYORDERF) bgrParser_sort );
intervalFind_addIntervalsToSearchSpace ( argv[1], 0 );
intervals = intervalFind_getAllIntervals ();
for( i=0; i<arrayMax(intervals); i++ ) {
Interval *currInterval = arrp( intervals, i, Interval );
length = currInterval->end - currInterval->start;
entries = bgrParser_getValuesForRegion( bgrs, currInterval->chromosome, currInterval->start, currInterval->end);
value = 0.0;
for( j=0; j<arrayMax( entries ); j++)
value += arru( entries, j, double );
printf("%s\t%s:%d-%d\t%f\n", currInterval->name,
currInterval->chromosome,
currInterval->start+1,
currInterval->end,
value /= length / 1000.0 );
arrayDestroy( entries );
}
arrayDestroy( intervals );
return 0;
}
void pbwtDestroy (PBWT *p)
{
if (p->chrom) free (p->chrom) ;
if (p->sites) arrayDestroy (p->sites) ;
if (p->samples) arrayDestroy (p->samples) ;
if (p->yz) arrayDestroy (p->yz) ;
if (p->zz) arrayDestroy (p->zz) ;
if (p->aFstart) free (p->aFstart) ;
if (p->aFend) free (p->aFend) ;
if (p->aRstart) free (p->aRstart) ;
if (p->aRend) free (p->aRend) ;
if (p->missingOffset) arrayDestroy (p->missingOffset) ;
if (p->zMissing) arrayDestroy (p->zMissing) ;
if (p->dosageOffset) arrayDestroy (p->dosageOffset) ;
if (p->zDosage) arrayDestroy (p->zDosage) ;
free (p) ;
}
static void blastParser_freeQuery (BlastQuery *currBlastQuery)
{
int i;
BlastEntry *currBlastEntry;
if (currBlastQuery == NULL) {
return;
}
hlr_free (currBlastQuery->qName);
for (i = 0; i < arrayMax (currBlastQuery->entries); i++) {
currBlastEntry = arrp (currBlastQuery->entries,i,BlastEntry);
hlr_free (currBlastEntry->tName);
}
arrayDestroy (currBlastQuery->entries);
freeMem (currBlastQuery);
}
static char* getBreakPointSequence (char *tileCoordinate1, char *tileCoordinate2)
{
Stringa buffer;
Stringa targetsFile;
FILE *fp;
Array targetSeqs;
int i;
Seq *currSeq;
static Stringa sequence = NULL;
buffer = stringCreate (100);
targetsFile = stringCreate (100);
stringPrintf (targetsFile,"targets_%d.txt",getpid ());
if (!(fp = fopen (string (targetsFile),"w")) ){
die ("Unable to open target file: %s",string (targetsFile));
}
fprintf (fp,"%s\n%s",tileCoordinate1,tileCoordinate2);
fclose (fp);
stringPrintf (buffer,"%s %s/%s stdout -noMask -seqList=%s",
confp_get(Conf, "BLAT_TWO_BIT_TO_FA"),
confp_get(Conf, "BLAT_DATA_DIR"),
confp_get(Conf, "BLAT_TWO_BIT_DATA_FILENAME"),
string (targetsFile));
fasta_initFromPipe (string (buffer));
targetSeqs = fasta_readAllSequences (0);
fasta_deInit ();
if (arrayMax (targetSeqs) != 2) {
die ("Expected only two target sequences");
}
stringCreateClear (sequence,100);
for (i = 0; i < arrayMax (targetSeqs); i++) {
currSeq = arrp (targetSeqs,i,Seq);
stringAppendf (sequence,"%s",currSeq->sequence);
hlr_free (currSeq->name);
hlr_free (currSeq->sequence);
}
arrayDestroy (targetSeqs);
stringPrintf (buffer,"rm -rf %s",string (targetsFile));
hlr_system (string (buffer),0);
stringDestroy (targetsFile);
stringDestroy (buffer);
return string (sequence);
}
SEXP c_read_biokit_exprs (SEXP filename) {
LineStream ls;
char* line;
const int MAND_NCOL=7; // the first column is the row name, and column 2-7 are mandatory
int add_ncol=0;
Texta it;
Texta rnames=textCreate(128);
Array mrpkms=arrayCreate(128, double);
Array mreads=arrayCreate(128, int);
Array srpkms=arrayCreate(128, double);
Array sreads=arrayCreate(128, int);
Array mprop=arrayCreate(128, double);
Array allmap = arrayCreate(128, int);
Array annos=arrayCreate(128, Texta);
Texta anno=NULL; // must have a NULL assigned; otherwise textCreateClear leads to memory error
Stringa str=stringCreate(8);
SEXP R_rnames, R_mrpkms, R_mreads, R_srpkms, R_sreads, R_mprop, R_allmap, R_res;
SEXP R_colnames, R_class;
int nprot=0;
int i=0;
int j=0;
int nrow=0;
const char* fn=CHAR(STRING_ELT(filename, 0));
ls = ls_createFromFile(strdup(fn));
ls_nextLine(ls); // skip the first header line
while(line = ls_nextLine(ls)) {
it = textFieldtokP(line, "\t");
if(arrayMax(it)<MAND_NCOL)
error("Input file must contain no less than %d columns", MAND_NCOL);
textAdd(rnames, textItem(it, 0));
array(mrpkms, arrayMax(mrpkms), double)=atof(textItem(it, 1));
array(mreads, arrayMax(mreads), int)=atoi(textItem(it, 2));
array(srpkms, arrayMax(srpkms), double)=atof(textItem(it, 3));
array(sreads, arrayMax(sreads), int)=atoi(textItem(it, 4));
array(mprop, arrayMax(mprop), double)=atof(textItem(it, 5));
array(allmap, arrayMax(allmap), int)=atoi(textItem(it, 6));
add_ncol = max(arrayMax(it)-MAND_NCOL, add_ncol);
textCreateClear(anno, arrayMax(it)-MAND_NCOL);
for(i=MAND_NCOL; i<arrayMax(it); ++i) {
textAdd(anno, textItem(it, i));
}
array(annos, arrayMax(annos), Texta)=textClone(anno);
nrow++;
}
R_rnames=PROTECT(allocVector(STRSXP, nrow)); nprot++;
R_mrpkms=PROTECT(allocVector(REALSXP, nrow)); nprot++;
R_mreads=PROTECT(allocVector(INTSXP, nrow)); nprot++;
R_srpkms=PROTECT(allocVector(REALSXP, nrow)); nprot++;
R_sreads=PROTECT(allocVector(INTSXP, nrow)); nprot++;
R_mprop=PROTECT(allocVector(REALSXP, nrow)); nprot++;
R_allmap=PROTECT(allocVector(INTSXP, nrow)); nprot++;
for(i=0; i<nrow; ++i) {
SET_STRING_ELT(R_rnames, i, mkChar(textItem(rnames, i)));
REAL(R_mrpkms)[i]=arru(mrpkms, i, double);
INTEGER(R_mreads)[i]=arru(mreads, i, int);
REAL(R_srpkms)[i]=arru(srpkms, i, double);
INTEGER(R_sreads)[i]=arru(sreads, i, int);
REAL(R_mprop)[i]=arru(mprop, i, double);
INTEGER(R_allmap)[i]=arru(allmap, i, int);
}
R_res=PROTECT(allocVector(VECSXP, MAND_NCOL+add_ncol-1)); nprot++;
SET_VECTOR_ELT(R_res, 0, R_mrpkms);
SET_VECTOR_ELT(R_res, 1, R_mreads);
SET_VECTOR_ELT(R_res, 2, R_srpkms);
SET_VECTOR_ELT(R_res, 3, R_sreads);
SET_VECTOR_ELT(R_res, 4, R_mprop);
SET_VECTOR_ELT(R_res, 5, R_allmap);
for(i=0; i<add_ncol; ++i) {
SEXP R_anno=NULL;
R_anno=PROTECT(allocVector(STRSXP, nrow));
for(j=0; j<nrow; ++j) {
anno=array(annos, j, Texta);
if(arrayMax(anno)>i) {
SET_STRING_ELT(R_anno, j, mkChar(textItem(anno, i)));
} else {
SET_STRING_ELT(R_anno, j, R_NaString);
}
}
SET_VECTOR_ELT(R_res, i+MAND_NCOL-1, R_anno); // -1 because the first column is row name
UNPROTECT(1);
}
PROTECT(R_colnames=allocVector(STRSXP, MAND_NCOL+add_ncol-1)); nprot++;
PROTECT(R_class=allocVector(STRSXP, 1)); nprot++;
SET_STRING_ELT(R_colnames, 0, mkChar("RPKM_MultiMap"));
SET_STRING_ELT(R_colnames, 1, mkChar("ReadCount_MultiMap"));
SET_STRING_ELT(R_colnames, 2, mkChar("RPKM_UniqMap"));
SET_STRING_ELT(R_colnames, 3, mkChar("ReadCount_UniqMap"));
SET_STRING_ELT(R_colnames, 4, mkChar("MultiProp"));
SET_STRING_ELT(R_colnames, 5, mkChar("AllMappingReads"));
for(i=0; i<add_ncol; ++i) {
stringPrintf(str, "Annotation%d", i+1);
SET_STRING_ELT(R_colnames, i+MAND_NCOL-1,
mkChar(string(str)));
}
SET_STRING_ELT(R_class, 0, mkChar("data.frame"));
setAttrib(R_res, install("names"), R_colnames);
setAttrib(R_res, install("row.names"), R_rnames);
setAttrib(R_res, install("class"), R_class);
for(i=0; i<nrow; ++i) {
textDestroy(array(annos, i, Texta));
}
arrayDestroy(annos);
arrayDestroy(rnames);
arrayDestroy(mrpkms);
arrayDestroy(mreads);
arrayDestroy(srpkms);
arrayDestroy(sreads);
arrayDestroy(mprop);
arrayDestroy(allmap);
stringDestroy(str);
ls_destroy(ls);
UNPROTECT(nprot);
return(R_res);
}
int main (int argc, char *argv[])
{
GfrEntry *currGE;
BLEntry *currBLE;
BLEntry currQuery;
FILE *fp;
char *line;
int count;
int countRemoved;
int index;
WordIter w;
Array blackList = arrayCreate(20, BLEntry);
if (argc != 2) {
usage ("%s <blackList.txt>",argv[0]);
}
fp = fopen( argv[1], "r" );
if( !fp ) die("Unable to open file: %s", argv[1]);
// reading blacklist file
LineStream ls = ls_createFromFile( argv[1] );
while( line = ls_nextLine(ls) ) {
w = wordIterCreate( line, "\t", 1);
currBLE = arrayp( blackList, arrayMax(blackList), BLEntry);
currBLE->gene1 = hlr_strdup ( wordNext(w) );
currBLE->gene2 = hlr_strdup ( wordNext(w) );
wordIterDestroy(w);
}
fclose(fp);
arraySort( blackList, (ARRAYORDERF) sortBlackListByName1);
// beginFiltering
count = 0;
countRemoved = 0;
gfr_init ("-");
puts (gfr_writeHeader ());
while (currGE = gfr_nextEntry ()) { // reading the gfr
// creating a new query to the black list
currQuery.gene1 = currGE->geneSymbolTranscript1;
currQuery.gene2 = currGE->geneSymbolTranscript2;
// searching against read_1/read_2
int res = arrayFind( blackList, &currQuery,
&index, (ARRAYORDERF) sortBlackListByName1);
if( !res ) { // not found, then searching against read_2/read_1
currQuery.gene1 = currGE->geneSymbolTranscript2;
currQuery.gene2 = currGE->geneSymbolTranscript1;
res = arrayFind( blackList, &currQuery,
&index, (ARRAYORDERF) sortBlackListByName1 );
if( !res ) { // not found, write the instance to stdout, update the counts
puts (gfr_writeGfrEntry (currGE));
count++;
} else { // found: read2/read1
countRemoved++;
}
} else { //found: read1/read2
countRemoved++;
}
}
gfr_deInit ();
arrayDestroy( blackList );
warn ("%s_BlackListFilter: %s",argv[0], argv[1]);
warn ("%s_numRemoved: %d",argv[0],countRemoved);
warn ("%s_numGfrEntries: %d",argv[0],count);
return 0;
}
void updateMagneticField(const RenderContext* context) {
static const Vector minCellPosRel = { -48, -48, -48 };
static const Vector maxCellPosRel = { 48, 48, 48 };
static const int cellStep = 8;
Vector minCellPos = vectorSum(context->camera.position, minCellPosRel);
Vector maxCellPos = vectorSum(context->camera.position, maxCellPosRel);
size_t i, count;
// remove points which is too far from camera
for (i = 0, count = arrayGetLength(_fieldPoints); i < count; ++i) {
pthread_mutex_lock(&_fieldPointsMutex);
VectorFieldPoint* point = (VectorFieldPoint*) arrayGetAt(_fieldPoints, i);
if (point->position.x < minCellPos.x + minCellPosRel.x || point->position.x > maxCellPos.x + maxCellPosRel.x ||
point->position.y < minCellPos.y + minCellPosRel.y || point->position.y > maxCellPos.y + maxCellPosRel.y ||
point->position.z < minCellPos.z + minCellPosRel.z || point->position.z > maxCellPos.z + maxCellPosRel.z) {
arrayDestroy(_fieldPoints, i);
--i;
--count;
}
pthread_mutex_unlock(&_fieldPointsMutex);
}
// compute points
int x, y, z;
for (x = (int) (minCellPos.x / cellStep) * cellStep; x <= maxCellPos.x; x += cellStep) {
for (y = (int) (minCellPos.y / cellStep) * cellStep; y <= maxCellPos.y; y += cellStep) {
for (z = (int) (minCellPos.z / cellStep) * cellStep; z <= maxCellPos.z; z += cellStep) {
const Vector position = { x, y, z };
// try to find
int pointExists = 0;
for (i = 0, count = arrayGetLength(_fieldPoints); i < count; ++i) {
pthread_mutex_lock(&_fieldPointsMutex);
VectorFieldPoint* point = (VectorFieldPoint*) arrayGetAt(_fieldPoints, i);
if (point->position.x >= x && point->position.x <= x + cellStep &&
point->position.y >= y && point->position.y <= y + cellStep &&
point->position.z >= z && point->position.z <= z + cellStep) {
pointExists = 1;
pthread_mutex_unlock(&_fieldPointsMutex);
break;
}
pthread_mutex_unlock(&_fieldPointsMutex);
}
if (pointExists) {
continue;
}
// compute if not exist
VectorFieldPoint* result = (VectorFieldPoint*) malloc(sizeof(VectorFieldPoint));
result->position = position;
result->direction = vectorZero;
for (i = 0, count = arrayGetLength(_conductors); i < count; ++i) {
Conductor* conductor = (Conductor*) arrayGetAt(_conductors, i);
result->direction = vectorSum(
result->direction,
calculateMagneticFieldPoint(conductor->I, conductor->permeability, conductor->l, vectorSubstract(position, conductor->position))
);
}
pthread_mutex_lock(&_fieldPointsMutex);
arrayAppend(_fieldPoints, result);
pthread_mutex_unlock(&_fieldPointsMutex);
}
}
}
}
int main (int argc, char *argv[])
{
GfrEntry *currGE;
BLEntry *currBLE;
BLEntry currQuery;
FILE *fp;
char *line;
int count;
int countRemoved;
int index;
WordIter w;
Array blackList = arrayCreate(20, BLEntry);
config *Conf;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL) {
die("%s:\tCannot find .fusionseqrc: %s", argv[0], getenv("FUSIONSEQ_CONFPATH"));
return EXIT_FAILURE;
}
if( confp_get( Conf, "ANNOTATION_DIR")==NULL ) {
die("%s:\tCannot find ANNOTATION_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( Conf, "BLACKLIST_FILENAME")==NULL ) {
die("%s:\tCannot find BLACKLIST_FILENAME in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
Stringa buffer=stringCreate( 100 );
stringPrintf( buffer, "%s/%s", confp_get( Conf, "ANNOTATION_DIR"), confp_get( Conf, "BLACKLIST_FILENAME") );
/* fp = fopen( string( buffer ), "r" );
if( !fp ) die("Unable to open file: %s", string(buffer));
stringDestroy( buffer );
*/
// reading blacklist file
LineStream ls = ls_createFromFile( string(buffer) );
while( line = ls_nextLine(ls) ) {
w = wordIterCreate( line, "\t", 1);
currBLE = arrayp( blackList, arrayMax(blackList), BLEntry);
currBLE->gene1 = hlr_strdup ( wordNext(w) );
currBLE->gene2 = hlr_strdup ( wordNext(w) );
wordIterDestroy(w);
}
//fclose(fp);
ls_destroy( ls );
stringDestroy( buffer );
arraySort( blackList, (ARRAYORDERF) sortBlackListByName1);
// beginFiltering
count = 0;
countRemoved = 0;
gfr_init ("-");
puts (gfr_writeHeader ());
while (currGE = gfr_nextEntry ()) { // reading the gfr
if( currGE->geneSymbolTranscript1 == NULL ) {
die("Gene symbols are not present in the GFR file. Please run gfrAddInfo before gfrBlackListFilter.");
return EXIT_FAILURE;
}
// creating a new query to the black list
currQuery.gene1 = currGE->geneSymbolTranscript1;
currQuery.gene2 = currGE->geneSymbolTranscript2;
if( strEqual( currQuery.gene1 , currQuery.gene2 ) ) {
countRemoved++;
continue;
}
// searching against read_1/read_2
int res = arrayFind( blackList, &currQuery,
&index, (ARRAYORDERF) sortBlackListByName1);
if( !res ) { // not found, then searching against read_2/read_1
currQuery.gene1 = currGE->geneSymbolTranscript2;
currQuery.gene2 = currGE->geneSymbolTranscript1;
res = arrayFind( blackList, &currQuery,
&index, (ARRAYORDERF) sortBlackListByName1 );
if( !res ) { // not found, write the instance to stdout, update the counts
puts (gfr_writeGfrEntry (currGE));
count++;
} else { // found: read2/read1
countRemoved++;
}
} else { //found: read1/read2
countRemoved++;
}
}
gfr_deInit ();
arrayDestroy( blackList );
warn ("%s_BlackListFilter: %s",argv[0], confp_get( Conf, "BLACKLIST_FILENAME"));
warn ("%s_numRemoved: %d",argv[0],countRemoved);
warn ("%s_numGfrEntries: %d",argv[0],count);
confp_close( Conf);
return 0;
}