void printFasta(FILE* f, GStr& defline, char* seq, int seqlen) {
if (seq==NULL) return;
int len=(seqlen>0)?seqlen:strlen(seq);
if (len<=0) return;
if (!defline.is_empty())
fprintf(f, ">%s\n",defline.chars());
int ilen=0;
for (int i=0; i < len; i++, ilen++) {
if (ilen == 70) {
fputc('\n', f);
ilen = 0;
}
putc(seq[i], f);
} //for
fputc('\n', f);
}
void collectLocusData(GList<GenomicSeqData>& ref_data) {
int locus_num=0;
for (int g=0;g<ref_data.Count();g++) {
GenomicSeqData* gdata=ref_data[g];
for (int l=0;l<gdata->loci.Count();l++) {
GffLocus& loc=*(gdata->loci[l]);
GHash<int> gnames(true); //gene names in this locus
GHash<int> geneids(true); //Entrez GeneID: numbers
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
GStr gname(t.getGeneName());
if (!gname.is_empty()) {
gname.upper();
int* prevg=gnames.Find(gname.chars());
if (prevg!=NULL) (*prevg)++;
else gnames.Add(gname, new int(1));
}
//parse GeneID xrefs, if any:
GStr xrefs(t.getAttr("xrefs"));
if (!xrefs.is_empty()) {
xrefs.startTokenize(",");
GStr token;
while (xrefs.nextToken(token)) {
token.upper();
if (token.startsWith("GENEID:")) {
token.cut(0,token.index(':')+1);
int* prevg=geneids.Find(token.chars());
if (prevg!=NULL) (*prevg)++;
else geneids.Add(token, new int(1));
}
} //for each xref
} //xrefs parsing
}//for each transcript
locus_num++;
loc.locus_num=locus_num;
if (gnames.Count()>0) { //collect all gene names associated to this locus
gnames.startIterate();
int* gfreq=NULL;
char* key=NULL;
while ((gfreq=gnames.NextData(key))!=NULL) {
loc.gene_names.AddIfNew(new CGeneSym(key,*gfreq));
}
} //added collected gene_names
if (loc.gene_ids.Count()>0) { //collect all GeneIDs names associated to this locus
geneids.startIterate();
int* gfreq=NULL;
char* key=NULL;
while ((gfreq=geneids.NextData(key))!=NULL) {
loc.gene_ids.AddIfNew(new CGeneSym(key,*gfreq));
}
}
} //for each locus
}//for each genomic sequence
}
void read_mRNAs(FILE* f, GList<GSeqData>& seqdata, GList<GSeqData>* ref_data,
int check_for_dups, int qfidx, const char* fname, bool only_multiexon) {
//>>>>> read all transcripts/features from a GTF/GFF3 file
//int imrna_counter=0;
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("00");
#endif
int loci_counter=0;
if (ref_data==NULL) ref_data=&seqdata;
bool isRefData=(&seqdata==ref_data);
//(f, transcripts_only)
GffReader* gffr=new GffReader(f, true); //load only transcript annotations
gffr->showWarnings(gtf_tracking_verbose);
// keepAttrs mergeCloseExons noExonAttrs
gffr->readAll(!isRefData, true, isRefData || gtf_tracking_largeScale);
//so it will read exon attributes only for low number of Cufflinks files
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_readAll");
#endif
int d=parse_mRNAs(gffr->gflst, seqdata, isRefData, check_for_dups, qfidx,only_multiexon);
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_parse_mRNAs");
#endif
if (gtf_tracking_verbose && d>0) {
if (isRefData) GMessage(" %d duplicate reference transcripts discarded.\n",d);
else GMessage(" %d redundant cufflinks transfrags discarded.\n",d);
}
//imrna_counter=gffr->mrnas.Count();
delete gffr; //free the extra memory and unused GffObjs
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_del_gffr");
#endif
//for each genomic sequence, cluster transcripts
int discarded=0;
GStr bname(fname);
GStr s;
if (!bname.is_empty()) {
int di=bname.rindex('.');
if (di>0) bname.cut(di);
int p=bname.rindex('/');
if (p<0) p=bname.rindex('\\');
if (p>=0) bname.remove(0,p);
}
FILE* fdis=NULL;
FILE* frloci=NULL;
for (int g=0;g<seqdata.Count();g++) {
//find the corresponding refseqdata with the same gseq_id
int gseq_id=seqdata[g]->get_gseqid();
if (!isRefData) { //cufflinks data, find corresponding ref data
GSeqData* rdata=getRefData(gseq_id, *ref_data);
if (rdata!=NULL && seqdata[g]->umrnas.Count()>0) {
discarded+=fix_umrnas(*seqdata[g], rdata, fdis);
}
}
//>>>>> group mRNAs into locus-clusters (based on exon overlap)
cluster_mRNAs(seqdata[g]->mrnas_f, seqdata[g]->loci_f, qfidx);
cluster_mRNAs(seqdata[g]->mrnas_r, seqdata[g]->loci_r, qfidx);
if (!isRefData) {
cluster_mRNAs(seqdata[g]->umrnas, seqdata[g]->nloci_u, qfidx);
}
loci_counter+=seqdata[g]->loci_f.Count();
loci_counter+=seqdata[g]->loci_r.Count();
// if (refData) {
// if (frloci==NULL) {
// s=bname;
// s.append(".loci.lst");
// frloci=fopen(s.chars(), "w");
// }
// writeLoci(frloci, seqdata[g]->loci_f);
// writeLoci(frloci, seqdata[g]->loci_r);
// }//write ref loci
}//for each genomic sequence
if (fdis!=NULL) fclose(fdis);
if (frloci!=NULL) fclose(frloci);
if (discarded>0) {
if (gtf_tracking_verbose) GMessage("Found %d transcripts with undetermined strand.\n", discarded);
}
else { if (fdis!=NULL) remove(s.chars()); }
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_cluster");
#endif
}
int main(int argc, char * const argv[]) {
GArgs args(argc, argv,
"debug;merge;cluster-only;help;force-exons;no-pseudo;MINCOV=MINPID=hvOUNHWCVJMKQNSXTDAPRZFGLEm:g:i:r:s:t:a:b:o:w:x:y:d:");
args.printError(USAGE, true);
if (args.getOpt('h') || args.getOpt("help")) {
GMessage("%s",USAGE);
exit(1);
}
debugMode=(args.getOpt("debug")!=NULL);
decodeChars=(args.getOpt('D')!=NULL);
forceExons=(args.getOpt("force-exons")!=NULL);
NoPseudo=(args.getOpt("no-pseudo")!=NULL);
mRNAOnly=(args.getOpt('O')==NULL);
//sortByLoc=(args.getOpt('S')!=NULL);
addDescr=(args.getOpt('A')!=NULL);
verbose=(args.getOpt('v')!=NULL);
wCDSonly=(args.getOpt('C')!=NULL);
validCDSonly=(args.getOpt('V')!=NULL);
altPhases=(args.getOpt('H')!=NULL);
fmtGTF=(args.getOpt('T')!=NULL); //switch output format to GTF
bothStrands=(args.getOpt('B')!=NULL);
fullCDSonly=(args.getOpt('J')!=NULL);
spliceCheck=(args.getOpt('N')!=NULL);
bool matchAllIntrons=(args.getOpt('K')==NULL);
bool fuzzSpan=(args.getOpt('Q')!=NULL);
if (args.getOpt('M') || args.getOpt("merge")) {
doCluster=true;
doCollapseRedundant=true;
}
else {
if (!matchAllIntrons || fuzzSpan) {
GMessage("%s",USAGE);
GMessage("Error: -K or -Q options require -M/--merge option!\n");
exit(1);
}
}
if (args.getOpt("cluster-only")) {
doCluster=true;
doCollapseRedundant=false;
if (!matchAllIntrons || fuzzSpan) {
GMessage("%s",USAGE);
GMessage("Error: -K or -Q options have no effect with --cluster-only.\n");
exit(1);
}
}
if (fullCDSonly) validCDSonly=true;
if (verbose) {
fprintf(stderr, "Command line was:\n");
args.printCmdLine(stderr);
}
fullattr=(args.getOpt('F')!=NULL);
if (args.getOpt('G')==NULL)
noExonAttr=!fullattr;
else {
noExonAttr=true;
fullattr=true;
}
if (NoPseudo && !fullattr) {
noExonAttr=true;
fullattr=true;
}
ensembl_convert=(args.getOpt('L')!=NULL);
if (ensembl_convert) {
fullattr=true;
noExonAttr=false;
//sortByLoc=true;
}
mergeCloseExons=(args.getOpt('Z')!=NULL);
multiExon=(args.getOpt('U')!=NULL);
writeExonSegs=(args.getOpt('W')!=NULL);
tracklabel=args.getOpt('t');
GFastaDb gfasta(args.getOpt('g'));
//if (gfasta.fastaPath!=NULL)
// sortByLoc=true; //enforce sorting by chromosome/contig
GStr s=args.getOpt('i');
if (!s.is_empty()) maxintron=s.asInt();
FILE* f_repl=NULL;
s=args.getOpt('d');
if (!s.is_empty()) {
if (s=="-") f_repl=stdout;
else {
f_repl=fopen(s.chars(), "w");
if (f_repl==NULL) GError("Error creating file %s\n", s.chars());
}
}
rfltWithin=(args.getOpt('R')!=NULL);
s=args.getOpt('r');
if (!s.is_empty()) {
s.trim();
if (s[0]=='+' || s[0]=='-') {
rfltStrand=s[0];
s.cut(0,1);
}
int isep=s.index(':');
if (isep>0) { //gseq name given
if (rfltStrand==0 && (s[isep-1]=='+' || s[isep-1]=='-')) {
isep--;
rfltStrand=s[isep];
s.cut(isep,1);
}
if (isep>0)
rfltGSeq=Gstrdup((s.substr(0,isep)).chars());
s.cut(0,isep+1);
}
GStr gsend;
char slast=s[s.length()-1];
if (rfltStrand==0 && (slast=='+' || slast=='-')) {
s.chomp(slast);
rfltStrand=slast;
}
if (s.index("..")>=0) gsend=s.split("..");
else gsend=s.split('-');
if (!s.is_empty()) rfltStart=(uint)s.asInt();
if (!gsend.is_empty()) {
rfltEnd=(uint)gsend.asInt();
if (rfltEnd==0) rfltEnd=MAX_UINT;
}
} //gseq/range filtering
else {
if (rfltWithin)
GError("Error: option -R requires -r!\n");
//if (rfltWholeTranscript)
// GError("Error: option -P requires -r!\n");
}
s=args.getOpt('m');
if (!s.is_empty()) {
FILE* ft=fopen(s,"r");
if (ft==NULL) GError("Error opening reference table: %s\n",s.chars());
loadRefTable(ft, reftbl);
fclose(ft);
}
s=args.getOpt('s');
if (!s.is_empty()) {
FILE* fsize=fopen(s,"r");
if (fsize==NULL) GError("Error opening info file: %s\n",s.chars());
loadSeqInfo(fsize, seqinfo);
fclose(fsize);
}
openfw(f_out, args, 'o');
//if (f_out==NULL) f_out=stdout;
if (gfasta.fastaPath==NULL && (validCDSonly || spliceCheck || args.getOpt('w')!=NULL || args.getOpt('x')!=NULL || args.getOpt('y')!=NULL))
GError("Error: -g option is required for options -w, -x, -y, -V, -N, -M !\n");
openfw(f_w, args, 'w');
openfw(f_x, args, 'x');
openfw(f_y, args, 'y');
if (f_y!=NULL || f_x!=NULL) wCDSonly=true;
//useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);
int numfiles = args.startNonOpt();
//GList<GffObj> gfkept(false,true); //unsorted, free items on delete
int out_counter=0; //number of records printed
while (true) {
GStr infile;
if (numfiles) {
infile=args.nextNonOpt();
if (infile.is_empty()) break;
if (infile=="-") { f_in=stdin; infile="stdin"; }
else
if ((f_in=fopen(infile, "r"))==NULL)
GError("Error: cannot open input file %s!\n",infile.chars());
}
else
infile="-";
GffLoader gffloader(infile.chars());
gffloader.transcriptsOnly=mRNAOnly;
gffloader.fullAttributes=fullattr;
gffloader.noExonAttrs=noExonAttr;
gffloader.mergeCloseExons=mergeCloseExons;
gffloader.showWarnings=(args.getOpt('E')!=NULL);
gffloader.noPseudo=NoPseudo;
gffloader.load(g_data, &validateGffRec, doCluster, doCollapseRedundant,
matchAllIntrons, fuzzSpan, forceExons);
if (doCluster)
collectLocusData(g_data);
if (numfiles==0) break;
}
GStr loctrack("gffcl");
if (tracklabel) loctrack=tracklabel;
g_data.setSorted(&gseqCmpName);
GffPrintMode exonPrinting;
if (fmtGTF) {
exonPrinting = pgtfAny;
} else {
exonPrinting = forceExons ? pgffBoth : pgffAny;
}
bool firstGff3Print=!fmtGTF;
if (doCluster) {
//grouped in loci
for (int g=0;g<g_data.Count();g++) {
GenomicSeqData* gdata=g_data[g];
int gfs_i=0;
for (int l=0;l<gdata->loci.Count();l++) {
GffLocus& loc=*(gdata->loci[l]);
//check all non-replaced transcripts in this locus:
int numvalid=0;
int idxfirstvalid=-1;
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
if (f_out) {
while (gfs_i<gdata->gfs.Count() && gdata->gfs[gfs_i]->start<=t.start) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
GTData* tdata=(GTData*)(t.uptr);
if (tdata->replaced_by!=NULL) {
if (f_repl && (t.udata & 8)==0) {
//t.udata|=8;
fprintf(f_repl, "%s", t.getID());
GTData* rby=tdata;
while (rby->replaced_by!=NULL) {
fprintf(f_repl," => %s", rby->replaced_by->getID());
rby->rna->udata|=8;
rby=(GTData*)(rby->replaced_by->uptr);
}
fprintf(f_repl, "\n");
}
continue;
}
if (process_transcript(gfasta, t)) {
t.udata|=4; //tag it as valid
numvalid++;
if (idxfirstvalid<0) idxfirstvalid=i;
}
}
if (f_out && numvalid>0) {
GStr locname("RLOC_");
locname.appendfmt("%08d",loc.locus_num);
if (!fmtGTF) {
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
fprintf(f_out,"%s\t%s\tlocus\t%d\t%d\t.\t%c\t.\tID=%s;locus=%s",
loc.rnas[0]->getGSeqName(), loctrack.chars(), loc.start, loc.end, loc.strand,
locname.chars(), locname.chars());
//const char* loc_gname=loc.getGeneName();
if (loc.gene_names.Count()>0) { //print all gene names associated to this locus
fprintf(f_out, ";genes=%s",loc.gene_names.First()->name.chars());
for (int i=1;i<loc.gene_names.Count();i++) {
fprintf(f_out, ",%s",loc.gene_names[i]->name.chars());
}
}
if (loc.gene_ids.Count()>0) { //print all GeneIDs names associated to this locus
fprintf(f_out, ";geneIDs=%s",loc.gene_ids.First()->name.chars());
for (int i=1;i<loc.gene_ids.Count();i++) {
fprintf(f_out, ",%s",loc.gene_ids[i]->name.chars());
}
}
fprintf(f_out, ";transcripts=%s",loc.rnas[idxfirstvalid]->getID());
for (int i=idxfirstvalid+1;i<loc.rnas.Count();i++) {
fprintf(f_out, ",%s",loc.rnas[i]->getID());
}
fprintf(f_out, "\n");
}
//now print all valid, non-replaced transcripts in this locus:
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
GTData* tdata=(GTData*)(t.uptr);
if (tdata->replaced_by!=NULL || ((t.udata & 4)==0)) continue;
t.addAttr("locus", locname.chars());
out_counter++;
if (fmtGTF) t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
else {
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
//print the parent first, if any
if (t.parent!=NULL && ((t.parent->udata & 4)==0)) {
GTData* pdata=(GTData*)(t.parent->uptr);
if (pdata && pdata->geneinfo!=NULL)
pdata->geneinfo->finalize();
t.parent->addAttr("locus", locname.chars());
t.parent->printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
t.parent->udata|=4;
}
t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
}
} //have valid transcripts to print
}//for each locus
//print the rest of the isolated pseudo/gene/region features not printed yet
if (f_out) {
while (gfs_i<gdata->gfs.Count()) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
} //for each genomic sequence
}
else {
//not grouped into loci, print the rnas with their parents, if any
int numvalid=0;
for (int g=0;g<g_data.Count();g++) {
GenomicSeqData* gdata=g_data[g];
int gfs_i=0;
for (int m=0;m<gdata->rnas.Count();m++) {
GffObj& t=*(gdata->rnas[m]);
if (f_out) {
while (gfs_i<gdata->gfs.Count() && gdata->gfs[gfs_i]->start<=t.start) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
GTData* tdata=(GTData*)(t.uptr);
if (tdata->replaced_by!=NULL) continue;
if (process_transcript(gfasta, t)) {
t.udata|=4; //tag it as valid
numvalid++;
if (f_out) {
if (tdata->geneinfo) tdata->geneinfo->finalize();
out_counter++;
if (fmtGTF) t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
else {
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
//print the parent first, if any
if (t.parent!=NULL && ((t.parent->udata & 4)==0)) {
GTData* pdata=(GTData*)(t.parent->uptr);
if (pdata && pdata->geneinfo!=NULL)
pdata->geneinfo->finalize();
t.parent->printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
t.parent->udata|=4;
}
t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
}//GFF/GTF output requested
} //valid transcript
} //for each rna
//print the rest of the isolated pseudo/gene/region features not printed yet
if (f_out) {
while (gfs_i<gdata->gfs.Count()) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
} //for each genomic seq
} //not clustered
if (f_repl && f_repl!=stdout) fclose(f_repl);
seqinfo.Clear();
//if (faseq!=NULL) delete faseq;
//if (gcdb!=NULL) delete gcdb;
GFREE(rfltGSeq);
FRCLOSE(f_in);
FWCLOSE(f_out);
FWCLOSE(f_w);
FWCLOSE(f_x);
FWCLOSE(f_y);
}
int main(int argc, char * const argv[]) {
//GArgs args(argc, argv, "hg:c:s:t:o:p:help;genomic-fasta=COV=PID=seq=out=disable-flag;test=");
GArgs args(argc, argv, opts);
fprintf(stderr, "Command line was:\n");
args.printCmdLine(stderr);
args.printError(USAGE, true);
//if (args.getOpt('h') || args.getOpt("help"))
if (args.getOpt(OPT_HELP))
{
GMessage("%s\n", USAGE);
exit(1);
}
if (args.getOpt(OPT_NUM)) {
GStr snum(args.getOpt(OPT_NUM));
int num=snum.asInt();
char* numstr=commaprintnum(num);
GMessage("Number %d written with commas: %s\n", num, numstr);
GFREE(numstr);
}
//---
GHash<GVec<int> > ends;
/*
testGPVec();
//exit(0);
//uint pos=3;
//GStr spos((int)pos);
//GVec<int> *ev=ends[spos.chars()];
GPVec<Gint> v;
int r(5);
int rr=v.Add(new Gint(3));
//if (rr<0) {
// GMessage("Error adding 0! (code %d)\n",rr);
// }
v.Add(new Gint(r));
v.Add(new Gint(2));
v.Add(new Gint(1));
v.Add(new Gint(4));
rr=v.Add(new Gint(0));
v[rr]->v=-1;
v.Sort(cmpGint);
GMessage("collection has %d elements:\n",v.Count());
for (int i=0;i<v.Count();i++) {
GMessage("v[%d]=%d;\n",i,v[i]->v);
}
exit(0);
*/
//---
int numopts=args.startOpt();
if (numopts)
GMessage("#### Recognized %d option arguments:\n", numopts);
int optcode=0;
while ((optcode=args.nextCode())) {
char* r=args.getOpt(optcode);
GMessage("%14s\t= %s\n", args.getOptName(optcode), (r[0]==0)?"True":r);
}
int numargs=args.startNonOpt();
if (numargs>0) {
GMessage("\n#### Found %d non-option arguments given:\n", numargs);
char* a=NULL;
while ((a=args.nextNonOpt())) {
GMessage("%s\n",a);
}
}
GStr s=args.getOpt('t');
if (!s.is_empty()) {
GStr token;
GMessage("Tokens in \"%s\" :\n",s.chars());
s.startTokenize(";,: \t");
int c=1;
while (s.nextToken(token)) {
GMessage("token %2d : \"%s\"\n",c,token.chars());
c++;
}
}
if (args.getOpt(OPT_BITVEC)) {
uint numbits=4156888234;
GBitVec bits(numbits);
GMessage(">>> -- BitVec(%u) created (size=%u, mem=%lu) -- \n", numbits, bits.size(),
bits.getMemorySize());
bits[405523342]=true;
GMessage(" memory size: %lu , size()=%u, count()=%d \n", bits.getMemorySize(), bits.size(), bits.count());
/*
//GMessage(">>> -- Start BitVec Test -- \n");
if (bits[1092]) bitError(1092);
bits.resize(2049);
if (bits[2048]) bitError(2048);
bits[2048]=true;
if (!bits[2048]) bitError(2048);
bits.resize(4097);
if (!bits[2048]) bitError(2048);
if (bits[4096]) bitError(4096);
bits[4096]=true;
if (!bits[4096]) bitError(4096);
GBitVec bits2(64);
Gswap(bits, bits2);
if (!bits2[2048]) bitError(2048);
if (!bits2[4096]) bitError(4096);
*/
//GMessage("<<< -- End BitVec Test (size: %d, count: %d, bits2 size=%d, count=%d) --\n",
/// bits.size(), bits.count(), bits2.size(), bits2.count());
}
}