/** \brief Set the argument offsets for a function, then kick off compiling
* of the function
*
* \param prevarg - Last argument
* \param currfn - Current function
*/
void setlocvar(SYMBOL *prevarg,SYMBOL *currfn)
{
int lgh,where;
int *iptr;
SYMBOL *copyarg;
int argnumber;
char buffer2[120];
unsigned char tester;
lgh = 0; /* Initialise it */
if ( prevarg != NULL && currfn->prototyped == 0 ) {
StoreFunctionSignature(prevarg);
}
argnumber=currfn->prototyped;
/*
* If we have filled up our number of arguments, then pretend
* we don't have any..nasty, nasty
*/
if (argnumber==(MAXARGS-1)) argnumber=0;
else if (argnumber) argnumber=1;
/*
* Dump some info about defining the function etc
*/
if (verbose){
toconsole();
outstr("Defining function: "); outstr(currfn->name); nl();
tofile();
}
nl();prefix();outname(currfn->name,dopref(currfn));col();nl(); /* print function name */
infunc=1; /* In a function for sure! */
copyarg=prevarg;
if ( ( (currfn->flags&SHARED) && makeshare ) || sharedfile ) {
/* Shared library definition, offset the stack */
where= 2 +shareoffset;
} else
where = 2 ;
/* If we use frame pointer we preserve previous framepointer on entry
* to each function
*/
#ifdef USEFRAME
if (useframe) where+=2;
#endif
while ( prevarg ) {
lgh = 2 ; /* Default length */
/* This is strange, previously double check for ->type */
if ( prevarg->type == LONG && prevarg->ident != POINTER )
lgh=4;
if ( prevarg->type == DOUBLE && prevarg->ident != POINTER )
lgh=6;
/* Far pointers */
if ( (prevarg->flags&FARPTR)==FARPTR && prevarg->ident == POINTER)
lgh=4;
prevarg->size=lgh;
#ifdef CODSWALLOP
/* All pointers are pushed onto the stack for functions as 4 bytes, if
* needed, near pointers are padded out to compensate for this by dummy
* loading with zero, this allows us to have one set of routines to
* cope with this and hence solve a lot of duplication
*/
if (prevarg->ident == POINTER && lpointer) lgh=4;
prevarg->size=lgh;
#endif
/*
* Check the definition against prototypes here...
*/
if (argnumber) {
tester=CalcArgValue(prevarg->type,prevarg->ident,prevarg->flags);
if (currfn->args[argnumber] != tester ) {
if (currfn->args[argnumber] != PELLIPSES ) {
if (currfn->args[argnumber] == 0 ) {
warning(W_2MADECL);
} else {
if ( (currfn->args[argnumber]&PMASKSIGN) == (tester&PMASKSIGN) ) {
warning(W_SIGNARG);
} else {
error(E_ARGMIS1,currfn->name,currfn->prototyped-argnumber+1, ExpandArgValue(tester,buffer2,prevarg->tag_idx) );
error(E_ARGMIS2,ExpandArgValue(currfn->args[argnumber],buffer2, currfn->tagarg[argnumber]));
}
}
}
}
argnumber++;
}
iptr = &prevarg->offset.i ;
prevarg = prevarg->offset.p ; /* follow ptr to prev. arg */
*iptr = where ; /* insert offset */
where += lgh ; /* calculate next offset */
}
#ifdef USEFRAME
pushframe();
#endif
currfn->handled=YES;
if (currfn->prototyped==1 && (currfn->flags®CALL) ) {
/*
* Fast call routine..
*/
if (lgh==2) zpush();
else if (lgh==4) lpush();
else if (lgh==6) dpush();
/* erk, if not matched, dodgy type! */
copyarg->offset.i=-lgh;
where=2;
}
stackargs=where;
lstdecl=0; /* Set number of local statics to zero */
if ( statement() != STRETURN ) {
if (lstdecl) postlabel(lstlab);
lstdecl=0;
/* do a statement, but if it's a return, skip */
/* cleaning up the stack */
leave(NO,NO) ;
}
CleanGoto();
/* Asz80 needs a label at the end to sort out local symbols */
if (asxx) {
nl();prefix();
outstr("smce_");
outname(currfn->name,NO);
col();nl();
}
#ifdef INBUILT_OPTIMIZER
generate();
#endif
infunc = 0 ; /* not in fn. any more */
}
int PET::write( int options ) {
int sl, fr;
ofstream outfile;
char outbuff[100];
string patid( getPatientID() );
string outname( getPatientID() );
string patname( _prefix );
cout << "PET::write(): " << _numFrame << " frames of " << _numSlice << " slices." << endl;
if ( options & OPT_VOLU ) {
// Using one output file.
// string outname( _prefix + "." );
// string outname( + "." );
outname.append( "." );
outname.append( (options & OPT_ANAL) ? "img" : "raw");
outfile.open( outname.c_str(), ios::binary );
if ( !outfile.is_open() )
error( "Cannot open output file", outname );
// Write the Analyze header if required.
if ( options & OPT_ANAL )
analyze->writePET( this, outname, options, 0 );
}
// Run through each frame and write to disk.
std::transform(patname.begin(), patname.end(), patname.begin(),
(int(*)(int)) toupper);
for ( fr = 0; fr < _numFrame; fr++ ) {
if ( !( options & OPT_VOLU )) {
// New output file per frame if not writing to one file.
// Changed this 4/2/07 ahc. Can't remember why I was using patid
// rather than abbreviated name for Analyze files.
// sprintf( outbuff, "%s_%02d.%s",
// patid.c_str(), fr, (options & OPT_ANAL) ? "img" : "raw" );
sprintf( outbuff, "%s_%02d.%s",
patname.c_str(), fr, (options & OPT_ANAL) ? "img" : "raw" );
outfile.open( outbuff, ios::binary );
if ( !outfile.is_open() )
error( "Cannot open output file", outbuff );
// Write the Analyze header if required.
if ( options & OPT_ANAL )
analyze->writePET( this, outbuff, options, fr );
}
// Call virtual fn. for specific PET slices.
for ( int sl = 0; sl < _numSlice; sl++ ) {
writeSliceData( fr, sl, outfile, options );
}
if ( !( options & OPT_VOLU ))
outfile.close();
cout << ((fr + 1) % 10) << flush;
}
cout << endl;
if ( outfile.is_open() )
outfile.close();
return 0;
}
bool
GBuildMakefileGenerator::writeMakefile(QTextStream &text)
{
QStringList tmp;
QString filename(Option::output.fileName());
QString pathtoremove(qmake_getpwd());
QString relpath(pathtoremove);
QString strtarget(project->first("TARGET"));
bool isnativebin = nativebins.contains(strtarget);
relpath.replace(Option::output_dir, "");
/* correct output for non-prl, non-recursive case */
QString outname(qmake_getpwd());
outname += QDir::separator();
outname += strtarget;
outname += projectSuffix();
Option::output.close();
Option::output.setFileName(outname);
MakefileGenerator::openOutput(Option::output, QString());
if (strtarget != fileInfo(project->projectFile()).baseName().section('.', -2, -2)) {
QString gpjname(strtarget);
QString outputName(qmake_getpwd());
outputName += QDir::separator();
outputName += fileInfo(project->projectFile()).baseName();
outputName += projectSuffix();
QFile f(outputName);
f.open(QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate);
QTextStream t(&f);
t << "#!gbuild\n";
t << "[Project]\n";
t << gpjname << projectSuffix() << "\n";
if ((project->first("TEMPLATE") == "lib")
&& project->isActiveConfig("shared"))
t << gpjname << "_shared" << projectSuffix() << "\n";
t.flush();
gpjname += projectSuffix();
Option::output.close();
Option::output.setFileName(gpjname);
MakefileGenerator::openOutput(Option::output, QString());
}
if ((project->first("TEMPLATE") == "app")
&& (!isnativebin)) {
QTextStream t(&Option::output);
QString intname(strtarget);
intname += ".int";
/* this is for bulding an INTEGRITY application.
* generate the .int integrate file and the .gpj INTEGRITY Application
* project file, then go on with regular files */
t << "#!gbuild" << "\n";
t << "[INTEGRITY Application]" << "\n";
t << "\t:binDirRelative=.\n";
t << "\t-o " << strtarget << "\n";
t << intname << "\n";
t << strtarget << "_app" << projectSuffix() << "\n";
t.flush();
/* generate integrate file */
QFile f(intname);
f.open(QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate);
QTextStream ti(&f);
ti << "# This is a file automatically generated by qmake" << "\n";
ti << "# Modifications will be lost next time you run qmake" << "\n";
ti << "Kernel" << "\n";
ti << "\tFilename\tDynamicDownload" << "\n";
ti << "EndKernel" << "\n" << "\n";
ti << "AddressSpace" << "\n";
ti << "\tName\t" << strtarget << "\n";
ti << "\tFilename\t" << strtarget << "_app" << "\n";
ti << "\tMemoryPoolSize\t0x100000" << "\n";
ti << "\tLanguage\tC++" << "\n";
/* FIXME : heap size is huge to be big enough for every example
* it should probably be tailored for each example, btu there is no
* good way to guess that */
ti << "\tHeapSize\t0x00D00000" << "\n";
ti << "\tTask\tInitial" << "\n";
ti << "\t\tStackSize\t0x30000" << "\n";
ti << "\t\tStartIt\tTrue" << "\n";
ti << "\tEndTask" << "\n";
ti << "EndAddressSpace" << "\n";
ti.flush();
/* change current project file to <projectname>_app.gpj and continue
* generation */
outname.insert(outname.lastIndexOf("."), "_app");
Option::output.close();
Option::output.setFileName(outname);
MakefileGenerator::openOutput(Option::output, QString());
} else if ((project->first("TEMPLATE") == "lib")
&& project->isActiveConfig("dll")) {
QString gpjname(strtarget);
gpjname += "_shared";
gpjname += projectSuffix();
QFile f(gpjname);
f.open(QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate);
QTextStream t(&f);
t << "#!gbuild\n"
"[Program]\n"
"\t-A libINTEGRITY.so\n"
"\t-A libc.so\n"
"\t-A libscxx.so\n"
"\t-A libQtCore.so\n"
"\t-e __ghsbegin_text\n"
"\t-startfile=-\n"
"\t:syslibraries=-\n"
"\t-Onolink\n";
t << "\t-o lib" << strtarget << ".so\n";
t << "\t-l" << strtarget << "\n";
t << "\t-extractall=-l" << strtarget << "\n";
t << "\t:outputDir=work/" << filename.section(QDir::separator(), 0, -1).remove(".gpj") << "\n";
t << strtarget << "_shared.ld\n";
t << "$(__OS_DIR)/intlib/sharedobjbssinit.c\n";
t.flush();
QFile fl(strtarget + "_shared.ld");
fl.open(QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate);
QTextStream tl(&fl);
tl << "CONSTANTS {\n"
" __INTEGRITY_MinPageAlign = 16K\n"
" __INTEGRITY_MaxPageAlign = 16K\n"
" __INTEGRITY_LibCBaseAddress = \n";
tl << dllbase << "\n";
tl << "}\n"
"-sec\n"
"{\n"
" .picbase __INTEGRITY_LibCBaseAddress :\n"
" .text :\n"
" .syscall :\n"
" .intercall :\n"
" .interfunc :\n"
" .secinfo :\n"
" .rodata align(16) :\n"
" .fixaddr :\n"
" .fixtype :\n"
" .rombeg :\n"
" .textchecksum :\n"
" // The above sections may be large. Leave a bigger gap for large pages.\n"
" .pidbase align(__INTEGRITY_MaxPageAlign) :\n"
" .sdabase :\n"
" .data :\n"
" .toc :\n"
" .opd :\n"
" .datachecksum :\n"
" .sbss : \n"
" .bss align(__INTEGRITY_MinPageAlign) :\n"
" .argsection(__INTEGRITY_MaxPageAlign) :\n"
" .heap : \n"
"}\n";
tl.flush();
dllbase += DLLOFFSET;
}
warn_msg(WarnParser, Option::output.fileName().toAscii());
QTextStream t(&Option::output);
QString primaryTarget;
if (!project->values("QMAKE_CXX").isEmpty())
primaryTarget = project->values("QMAKE_CXX").at(0);
pathtoremove += QDir::separator();
filename.remove(qmake_getpwd());
//HEADER
t << "#!gbuild" << "\n";
/* find the architecture out of the compiler name */
if (filename.endsWith("projects.gpj")) {
primaryTarget.remove(0, 5);
t << "macro QT_BUILD_DIR=%expand_path(.)\n";
t << "macro __OS_DIR=" << project->values("INTEGRITY_DIR").first() << "\n";
t << "primaryTarget=" << primaryTarget << "_integrity.tgt" << "\n";
t << "customization=util/integrity/qt.bod\n";
}
/* project type */
if (project->first("TEMPLATE") == "app") {
t << "[Program]" << "\n";
if (isnativebin) {
t << "\t:binDir=bin\n";
t << "\t-o " << strtarget << "\n";
} else {
t << "\t:binDirRelative=.\n";
t << "\t-o " << strtarget << "_app\n";
}
} else if (project->first("TEMPLATE") == "lib") {
t << "[Library]" << "\n";
t << "\t:binDir=lib" << "\n";
t << "\t-o lib" << strtarget << ".a" << "\n";
} else if (project->first("TEMPLATE") == "subdirs")
t << "[Project]" << "\n";
else
t << project->first("TEMPLATE") << "\n";
/* compilations options */
t << "\t:sourceDir=." << "\n";
t << "\t:outputDir=work" << relpath << "\n";
t << "\t-I${%expand_path(.)}/work" << relpath << "\n";
t << "\t--cxx_include_directory ${%expand_path(.)}/work" << relpath << "\n";
if (filename.endsWith("projects.gpj")) {
t << "\t:sourceDir=work\n";
t << "\t-Iwork\n";
t << "\t-Llib\n";
t << "\t";
QStringList &l = project->values("QMAKE_CXXFLAGS");
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
if ((*it).startsWith("-"))
t << "\n" << "\t" << (*it);
else
t << " " << (*it);
}
t << "\n";
}
t << "\n";
if (project->first("TEMPLATE") != "project")
t << varGlue("DEFINES", "\t-D", "\n\t-D", "\n");
t << "\t-I.\n\t-I" << specdir() << "\n";
t << varGlue("INCLUDEPATH", "\t-I", "\n\t-I", "\n");
t << "\t--cxx_include_directory .\n\t--cxx_include_directory " << specdir() << "\n";
t << varGlue("INCLUDEPATH", "\t--cxx_include_directory ", "\n\t--cxx_include_directory ", "\n");
if (project->first("TEMPLATE") == "app") {
/* include linker flags if it's an application */
QString src[] = { "QMAKE_LFLAGS", "QMAKE_FRAMEWORKPATH_FLAGS", "QMAKE_LIBDIR_FLAGS", "QMAKE_LIBS", "LIBS", QString() };
for (int i = 0; !src[i].isNull(); i++) {
/* skip target libraries for native tools */
if (isnativebin && (i == 0))
continue;
t << "\t";
QStringList &l = project->values(src[i]);
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
if ((*it).startsWith("-"))
t << "\n" << "\t" << (*it);
else
t << " " << (*it);
}
t << "\n";
}
}
/* first subdirectories/subprojects */
{
QStringList &l = project->values("SUBDIRS");
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
QString gpjname((*it));
/* avoid native tools */
if (nativebins.contains(gpjname.section("_", -1)))
continue;
if (!project->first((*it) + ".subdir").isEmpty())
gpjname = project->first((*it) + ".subdir");
/* some SUBDIRS are not actually subdirs, instead .pro files */
if (gpjname.endsWith(".pro"))
gpjname.chop(4);
else
gpjname += QDir::separator() + gpjname.section(QDir::separator(), -1);
gpjname += projectSuffix();
/* make relative */
if (!project->values("QT_SOURCE_TREE").isEmpty()) {
gpjname.replace(project->values("QT_SOURCE_TREE").first() + QDir::separator(), "");
}
t << gpjname << "\n";
}
}
{
QStringList &l = project->values("RESOURCES");
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
QString tmpstr((*it).replace(pathtoremove, ""));
t << tmpstr << "\t[Qt Resource]\n";
tmpstr = tmpstr.section(".", -2, -1).section(QDir::separator(), -1);
tmpstr.remove(".qrc");
t << "\t-name " << tmpstr << "\n";
tmpstr.insert(tmpstr.lastIndexOf(QDir::separator()) + 1, "qrc_");
tmpstr.append(".cpp");
t << "\t-o work/" << relpath << QDir::separator() << tmpstr << "\n";
}
}
{
QStringList &l = project->values("FORMS");
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
QString tmpstr((*it).replace(pathtoremove, ""));
t << tmpstr << "\t[Qt Dialog]\n";
tmpstr = tmpstr.section(".", 0, 0).section(QDir::separator(), -1);
tmpstr.insert(tmpstr.lastIndexOf(QDir::separator()) + 1, "ui_");
tmpstr.remove(".ui");
tmpstr.append(".h");
t << "\t-o work/" << relpath << QDir::separator() << tmpstr << "\n";
}
}
/* source files for this project */
QString src[] = { "HEADERS", "SOURCES", QString() };
for (int i = 0; !src[i].isNull(); i++) {
QStringList &l = project->values(src[i]);
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
if ((*it).isEmpty())
continue;
/* native tools aren't preprocessed */
if (!isnativebin)
t << writeOne((*it), pathtoremove);
else
t << (*it).remove(pathtoremove) << "\n";
}
}
t << "\n";
{
QStringList &l = project->values("GENERATED_SOURCES");
for (QStringList::Iterator it = l.begin(); it != l.end(); ++it) {
t << "work/" << relpath << QDir::separator() << (*it).section(QDir::separator(), -1) << "\n";
}
}
return true;
}
/*
* write information about function definition
*
* this is also done for static functions so we are able to check if
* they are called with proper argument types
*/
void
outfdef(sym_t *fsym, pos_t *posp, int rval, int osdef, sym_t *args)
{
int narg;
sym_t *arg;
/* reset the buffer */
outclr();
/*
* line number of .c source, 'd' for declaration, Id of current
* source (.c or .h), and line in current source
*
* we are already at the end of the function. If we are in the
* .c source, posp->p_line is correct, otherwise csrc_pos.p_line
* (for functions defined in header files).
*/
if (posp->p_file == csrc_pos.p_file) {
outint(posp->p_line);
} else {
outint(csrc_pos.p_line);
}
outchar('d');
outint(getfnid(posp->p_file));
outchar('.');
outint(posp->p_line);
/* flags */
/* both SCANFLIKE and PRINTFLIKE imply VARARGS */
if (prflstrg != -1) {
nvararg = prflstrg;
} else if (scflstrg != -1) {
nvararg = scflstrg;
}
if (nvararg != -1) {
outchar('v');
outint(nvararg);
}
if (scflstrg != -1) {
outchar('S');
outint(scflstrg);
}
if (prflstrg != -1) {
outchar('P');
outint(prflstrg);
}
nvararg = prflstrg = scflstrg = -1;
outchar('d');
if (rval)
/* has return value */
outchar('r');
if (llibflg)
/*
* mark it as used so lint2 does not complain about
* unused symbols in libraries
*/
outchar('u');
if (osdef)
/* old style function definition */
outchar('o');
if (fsym->s_scl == STATIC)
outchar('s');
/* name of function */
outname(fsym->s_name);
/* renamed name of function, if necessary */
if (fsym->s_rename) {
outchar('r');
outname(fsym->s_rename);
}
/* argument types and return value */
if (osdef) {
narg = 0;
for (arg = args; arg != NULL; arg = arg->s_nxt)
narg++;
outchar('f');
outint(narg);
for (arg = args; arg != NULL; arg = arg->s_nxt)
outtype(arg->s_type);
outtype(fsym->s_type->t_subt);
} else {
outtype(fsym->s_type);
}
}
/*
* write out all information necessary for lint2 to check function
* calls
*
* rvused is set if the return value is used (asigned to a variable)
* rvdisc is set if the return value is not used and not ignored
* (casted to void)
*/
void
outcall(tnode_t *tn, int rvused, int rvdisc)
{
tnode_t *args, *arg;
int narg, n, i;
int64_t q;
tspec_t t;
/* reset buffer */
outclr();
/*
* line number of .c source, 'c' for function call, Id of current
* source (.c or .h), and line in current source
*/
outint(csrc_pos.p_line);
outchar('c');
outint(getfnid(curr_pos.p_file));
outchar('.');
outint(curr_pos.p_line);
/*
* flags; 'u' and 'i' must be last to make sure a letter
* is between the numeric argument of a flag and the name of
* the function
*/
narg = 0;
args = tn->tn_right;
for (arg = args; arg != NULL; arg = arg->tn_right)
narg++;
/* informations about arguments */
for (n = 1; n <= narg; n++) {
/* the last argument is the top one in the tree */
for (i = narg, arg = args; i > n; i--, arg = arg->tn_right)
continue;
arg = arg->tn_left;
if (arg->tn_op == CON) {
if (isityp(t = arg->tn_type->t_tspec)) {
/*
* XXX it would probably be better to
* explizitly test the sign
*/
if ((q = arg->tn_val->v_quad) == 0) {
/* zero constant */
outchar('z');
} else if (msb(q, t, 0) == 0) {
/* positive if casted to signed */
outchar('p');
} else {
/* negative if casted to signed */
outchar('n');
}
outint(n);
}
} else if (arg->tn_op == AMPER &&
arg->tn_left->tn_op == STRING &&
arg->tn_left->tn_strg->st_tspec == CHAR) {
/* constant string, write all format specifiers */
outchar('s');
outint(n);
outfstrg(arg->tn_left->tn_strg);
}
}
/* return value discarded/used/ignored */
outchar(rvdisc ? 'd' : (rvused ? 'u' : 'i'));
/* name of the called function */
outname(tn->tn_left->tn_left->tn_sym->s_name);
/* types of arguments */
outchar('f');
outint(narg);
for (n = 1; n <= narg; n++) {
/* the last argument is the top one in the tree */
for (i = narg, arg = args; i > n; i--, arg = arg->tn_right)
continue;
outtype(arg->tn_left->tn_type);
}
/* expected type of return value */
outtype(tn->tn_type);
}
/*
* write information about a global declared/defined symbol
* with storage class extern
*
* informations about function definitions are written in outfdef(),
* not here
*/
void
outsym(sym_t *sym, scl_t sc, def_t def)
{
/*
* Static function declarations must also be written to the output
* file. Compatibility of function declarations (for both static
* and extern functions) must be checked in lint2. Lint1 can't do
* this, especially not, if functions are declared at block level
* before their first declaration at level 0.
*/
if (sc != EXTERN && !(sc == STATIC && sym->s_type->t_tspec == FUNC))
return;
/* reset buffer */
outclr();
/*
* line number of .c source, 'd' for declaration, Id of current
* source (.c or .h), and line in current source.
*/
outint(csrc_pos.p_line);
outchar('d');
outint(getfnid(sym->s_dpos.p_file));
outchar('.');
outint(sym->s_dpos.p_line);
/* flags */
switch (def) {
case DEF:
/* defined */
outchar('d');
break;
case TDEF:
/* tentative defined */
outchar('t');
break;
case DECL:
/* declared */
outchar('e');
break;
default:
lerror("outsym() 2");
}
if (llibflg && def != DECL) {
/*
* mark it as used so we get no warnings from lint2 about
* unused symbols in libraries.
*/
outchar('u');
}
if (sc == STATIC)
outchar('s');
/* name of the symbol */
outname(sym->s_name);
/* renamed name of symbol, if necessary */
if (sym->s_rename) {
outchar('r');
outname(sym->s_rename);
}
/* type of the symbol */
outtype(sym->s_type);
}
/*
* Write type into the output buffer.
*/
static void
outtype(type_t *tp)
{
int t, s, na;
tspec_t ts;
type_t **ap;
while (tp != NULL) {
if ((ts = tp->t_tspec) == INT && tp->t_isenum)
ts = ENUM;
switch (ts) {
case CHAR: t = 'C'; s = '\0'; break;
case SCHAR: t = 'C'; s = 's'; break;
case UCHAR: t = 'C'; s = 'u'; break;
case SHORT: t = 'S'; s = '\0'; break;
case USHORT: t = 'S'; s = 'u'; break;
case INT: t = 'I'; s = '\0'; break;
case UINT: t = 'I'; s = 'u'; break;
case LONG: t = 'L'; s = '\0'; break;
case ULONG: t = 'L'; s = 'u'; break;
case QUAD: t = 'Q'; s = '\0'; break;
case UQUAD: t = 'Q'; s = 'u'; break;
case FLOAT: t = 'D'; s = 's'; break;
case DOUBLE: t = 'D'; s = '\0'; break;
case LDOUBLE: t = 'D'; s = 'l'; break;
case VOID: t = 'V'; s = '\0'; break;
case PTR: t = 'P'; s = '\0'; break;
case ARRAY: t = 'A'; s = '\0'; break;
case ENUM: t = 'T'; s = 'e'; break;
case STRUCT: t = 'T'; s = 's'; break;
case UNION: t = 'T'; s = 'u'; break;
case FUNC:
if (tp->t_args != NULL && !tp->t_proto) {
t = 'f';
} else {
t = 'F';
}
s = '\0';
break;
default:
errx(1, "internal error: outtype() 1");
}
if (tp->t_const)
outchar('c');
if (tp->t_volatile)
outchar('v');
if (s != '\0')
outchar(s);
outchar(t);
if (ts == ARRAY) {
outint(tp->t_dim);
} else if (ts == ENUM || ts == STRUCT || ts == UNION) {
if (tp->t_istag) {
outint(1);
outname(tp->t_tag->h_name);
} else if (tp->t_istynam) {
outint(2);
outname(tp->t_tynam->h_name);
} else if (tp->t_isuniqpos) {
outint(3);
outint(tp->t_uniqpos.p_line);
outchar('.');
outint(tp->t_uniqpos.p_file);
outchar('.');
outint(tp->t_uniqpos.p_uniq);
} else
errx(1, "internal error: outtype() 2");
} else if (ts == FUNC && tp->t_args != NULL) {
na = 0;
for (ap = tp->t_args; *ap != NULL; ap++)
na++;
if (tp->t_vararg)
na++;
outint(na);
for (ap = tp->t_args; *ap != NULL; ap++)
outtype(*ap);
if (tp->t_vararg)
outchar('E');
}
tp = tp->t_subt;
}
}
int rapMapMap(int argc, char* argv[]) {
std::cerr << "RapMap Mapper\n";
std::string versionString = rapmap::version;
TCLAP::CmdLine cmd(
"RapMap Mapper",
' ',
versionString);
cmd.getProgramName() = "rapmap";
TCLAP::ValueArg<std::string> index("i", "index", "The location of the pseudoindex", true, "", "path");
TCLAP::ValueArg<std::string> read1("1", "leftMates", "The location of the left paired-end reads", false, "", "path");
TCLAP::ValueArg<std::string> read2("2", "rightMates", "The location of the right paired-end reads", false, "", "path");
TCLAP::ValueArg<std::string> unmatedReads("r", "unmatedReads", "The location of single-end reads", false, "", "path");
TCLAP::ValueArg<uint32_t> numThreads("t", "numThreads", "Number of threads to use", false, 1, "positive integer");
TCLAP::ValueArg<uint32_t> maxNumHits("m", "maxNumHits", "Reads mapping to more than this many loci are discarded", false, 200, "positive integer");
TCLAP::ValueArg<std::string> outname("o", "output", "The output file (default: stdout)", false, "", "path");
TCLAP::SwitchArg endCollectorSwitch("e", "endCollector", "Use the simpler (and faster) \"end\" collector as opposed to the more sophisticated \"skipping\" collector", false);
TCLAP::SwitchArg noout("n", "noOutput", "Don't write out any alignments (for speed testing purposes)", false);
cmd.add(index);
cmd.add(noout);
cmd.add(read1);
cmd.add(read2);
cmd.add(unmatedReads);
cmd.add(outname);
cmd.add(numThreads);
cmd.add(maxNumHits);
cmd.add(endCollectorSwitch);
auto consoleSink = std::make_shared<spdlog::sinks::stderr_sink_mt>();
auto consoleLog = spdlog::create("stderrLog", {consoleSink});
try {
cmd.parse(argc, argv);
bool pairedEnd = (read1.isSet() or read2.isSet());
if (pairedEnd and (read1.isSet() != read2.isSet())) {
consoleLog->error("You must set both the -1 and -2 arguments to align "
"paired end reads!");
std::exit(1);
}
if (pairedEnd and unmatedReads.isSet()) {
consoleLog->error("You cannot specify both paired-end and unmated "
"reads in the input!");
std::exit(1);
}
if (!pairedEnd and !unmatedReads.isSet()) {
consoleLog->error("You must specify input; either both paired-end "
"or unmated reads!");
std::exit(1);
}
std::string indexPrefix(index.getValue());
if (indexPrefix.back() != '/') {
indexPrefix += "/";
}
if (!rapmap::fs::DirExists(indexPrefix.c_str())) {
consoleLog->error("It looks like the index you provided [{}] "
"doesn't exist", indexPrefix);
std::exit(1);
}
IndexHeader h;
std::ifstream indexStream(indexPrefix + "header.json");
{
cereal::JSONInputArchive ar(indexStream);
ar(h);
}
indexStream.close();
if (h.indexType() != IndexType::PSEUDO) {
consoleLog->error("The index {} does not appear to be of the "
"appropriate type (pseudo)", indexPrefix);
std::exit(1);
}
RapMapIndex rmi;
rmi.load(indexPrefix);
std::cerr << "\n\n\n\n";
// from: http://stackoverflow.com/questions/366955/obtain-a-stdostream-either-from-stdcout-or-stdofstreamfile
// set either a file or cout as the output stream
std::streambuf* outBuf;
std::ofstream outFile;
bool haveOutputFile{false};
if (outname.getValue() == "") {
outBuf = std::cout.rdbuf();
} else {
outFile.open(outname.getValue());
outBuf = outFile.rdbuf();
haveOutputFile = true;
}
// Now set the output stream to the buffer, which is
// either std::cout, or a file.
std::ostream outStream(outBuf);
// Must be a power of 2
size_t queueSize{268435456};
spdlog::set_async_mode(queueSize);
auto outputSink = std::make_shared<spdlog::sinks::ostream_sink_mt>(outStream);
auto outLog = std::make_shared<spdlog::logger>("outLog", outputSink);
outLog->set_pattern("%v");
uint32_t nthread = numThreads.getValue();
std::unique_ptr<paired_parser> pairParserPtr{nullptr};
std::unique_ptr<single_parser> singleParserPtr{nullptr};
if (!noout.getValue()) {
rapmap::utils::writeSAMHeader(rmi, outLog);
}
SpinLockT iomutex;
{
ScopedTimer timer;
HitCounters hctrs;
consoleLog->info("mapping reads . . . \n\n\n");
if (pairedEnd) {
std::vector<std::thread> threads;
std::vector<std::string> read1Vec = rapmap::utils::tokenize(read1.getValue(), ',');
std::vector<std::string> read2Vec = rapmap::utils::tokenize(read2.getValue(), ',');
if (read1Vec.size() != read2Vec.size()) {
consoleLog->error("The number of provided files for "
"-1 and -2 must be the same!");
std::exit(1);
}
size_t numFiles = read1Vec.size() + read2Vec.size();
char** pairFileList = new char*[numFiles];
for (size_t i = 0; i < read1Vec.size(); ++i) {
pairFileList[2*i] = const_cast<char*>(read1Vec[i].c_str());
pairFileList[2*i+1] = const_cast<char*>(read2Vec[i].c_str());
}
size_t maxReadGroup{1000}; // Number of reads in each "job"
size_t concurrentFile{2}; // Number of files to read simultaneously
pairParserPtr.reset(new paired_parser(4 * nthread, maxReadGroup,
concurrentFile,
pairFileList, pairFileList+numFiles));
/** Create the threads depending on the collector type **/
if (endCollectorSwitch.getValue()) {
EndCollector endCollector(&rmi);
for (size_t i = 0; i < nthread; ++i) {
threads.emplace_back(processReadsPair<EndCollector, SpinLockT>,
pairParserPtr.get(),
std::ref(rmi),
std::ref(endCollector),
&iomutex,
outLog,
std::ref(hctrs),
maxNumHits.getValue(),
noout.getValue());
}
} else {
SkippingCollector skippingCollector(&rmi);
for (size_t i = 0; i < nthread; ++i) {
threads.emplace_back(processReadsPair<SkippingCollector, SpinLockT>,
pairParserPtr.get(),
std::ref(rmi),
std::ref(skippingCollector),
&iomutex,
outLog,
std::ref(hctrs),
maxNumHits.getValue(),
noout.getValue());
}
}
for (auto& t : threads) { t.join(); }
delete [] pairFileList;
} else {
std::vector<std::thread> threads;
std::vector<std::string> unmatedReadVec = rapmap::utils::tokenize(unmatedReads.getValue(), ',');
size_t maxReadGroup{1000}; // Number of reads in each "job"
size_t concurrentFile{1};
stream_manager streams( unmatedReadVec.begin(), unmatedReadVec.end(),
concurrentFile);
singleParserPtr.reset(new single_parser(4 * nthread,
maxReadGroup,
concurrentFile,
streams));
/** Create the threads depending on the collector type **/
if (endCollectorSwitch.getValue()) {
EndCollector endCollector(&rmi);
for (size_t i = 0; i < nthread; ++i) {
threads.emplace_back(processReadsSingle<EndCollector, SpinLockT>,
singleParserPtr.get(),
std::ref(rmi),
std::ref(endCollector),
&iomutex,
outLog,
std::ref(hctrs),
maxNumHits.getValue(),
noout.getValue());
}
} else {
SkippingCollector skippingCollector(&rmi);
for (size_t i = 0; i < nthread; ++i) {
threads.emplace_back(processReadsSingle<SkippingCollector, SpinLockT>,
singleParserPtr.get(),
std::ref(rmi),
std::ref(skippingCollector),
&iomutex,
outLog,
std::ref(hctrs),
maxNumHits.getValue(),
noout.getValue());
}
}
for (auto& t : threads) { t.join(); }
}
consoleLog->info("Done mapping reads.");
consoleLog->info("In total saw {} reads.", hctrs.numReads);
consoleLog->info("Final # hits per read = {}", hctrs.totHits / static_cast<float>(hctrs.numReads));
consoleLog->info("Discarded {} reads because they had > {} alignments",
hctrs.tooManyHits, maxNumHits.getValue());
consoleLog->info("flushing output");
outLog->flush();
}
if (haveOutputFile) {
outFile.close();
}
return 0;
} catch (TCLAP::ArgException& e) {
consoleLog->error("Exception [{}] when parsing argument {}", e.error(), e.argId());
return 1;
}
}
/*
* evaluate one initialiser
*
* if dump is TRUE, dump literal immediately
* save character string in litq to dump later
* this is used for structures and arrays of pointers to char, so that the
* struct or array is built immediately and the char strings are dumped later
*/
void init(int size, int ident, int *dim, int more, int dump, int is_struct)
{
int32_t value;
int sz; /* number of chars in queue */
/*
* djm 14/3/99 We have to rewrite this bit (ugh!) so that we store
* our literal in a temporary queue, then if needed, we then dump
* it out..
*/
if ((sz = qstr(&value)) != -1 ) {
sz++;
#if 0
if (ident == VARIABLE || (size != 1 && more != CCHAR))
error(E_ASSIGN);
#endif
#ifdef INIT_TEST
outstr("ident=");
outdec(ident);
outstr("size=");
outdec(size);
outstr("more=");
outdec(more);
outstr("dim=");
outdec(*dim);
outstr("sz=");
outdec(sz);
nl();
#endif
if (ident == ARRAY && more == 0) {
/*
* Dump the literals where they are, padding out as appropriate
*/
if (*dim != -1 && sz > *dim) {
/*
* Ooops, initialised to long a string!
*/
warning(W_INIT2LONG);
sz = *dim;
gltptr = sz;
*(glbq + sz - 1) = '\0'; /* Terminate string */
}
dumplits(((size == 1) ? 0 : size), NO, gltptr, glblab, glbq);
*dim -= sz;
gltptr = 0;
dumpzero(size, *dim);
return;
} else {
/*
* Store the literals in the queue!
*/
storeq(sz, glbq, &value);
gltptr = 0;
defword();
printlabel(litlab);
outbyte('+');
outdec(value);
nl();
--*dim;
return;
}
}
/*
* djm, catch label names in structures (for (*name)() initialisation
*/
else {
char sname[NAMEMAX + 1];
SYMBOL *ptr;
if (symname(sname) && strcmp(sname,"sizeof") ) { /* We have got something.. */
if ((ptr = findglb(sname))) {
/* Actually found sommat..very good! */
if (ident == POINTER || (ident == ARRAY && more)) {
defword();
outname(ptr->name, dopref(ptr));
nl();
--*dim;
} else if (ptr->type == ENUM) {
value = ptr->size;
goto constdecl;
} else {
error(E_DDECL);
}
} else
error(E_UNSYMB, sname);
} else if (rcmatch('}')) {
#if 0
dumpzero(size,*dim);
#endif
} else if (constexpr(&value, 1)) {
constdecl:
if (ident == POINTER) {
/* 24/1/03 dom - We want to be able to assign values to
pointers or they're a bit useless..
*/
#if 0
/* the only constant which can be assigned to a pointer is 0 */
if (value != 0)
warning(W_ASSPTR);
#endif
size = 2;
dump = YES;
}
if (dump) {
/* struct member or array of pointer to char */
if (size == 4) {
/* there appears to be a bug in z80asm regarding defl */
defbyte();
outdec((value % 65536UL) % 256);
outbyte(',');
outdec((value % 65536UL) / 256);
outbyte(',');
outdec((value / 65536UL) % 256);
outbyte(',');
outdec((value / 65536UL) / 256);
} else {
if (size == 1)
defbyte();
else
defword();
outdec(value);
}
nl();
/* Dump out a train of zeros as appropriate */
if (ident == ARRAY && more == 0) {
dumpzero(size,(*dim)-1);
}
} else
stowlit(value, size);
--*dim;
}
}
}
/*
* initialise global object
*/
int initials(char *sname,
int type, int ident, int dim, int more,
TAG_SYMBOL * tag, char zfar)
{
int size, desize = 0;
int olddim = dim;
if (cmatch('=')) {
/* initialiser present */
defstatic = 1; /* So no 2nd redefine djm */
gltptr = 0;
glblab = getlabel();
if (dim == 0)
dim = -1;
switch (type) {
case CCHAR:
size = 1;
break;
case LONG:
size = 4;
break;
case CINT:
default:
size = 2;
}
output_section("data_compiler"); // output_section("text");
prefix();
outname(sname, YES);
col();
nl();
if (cmatch('{')) {
/* aggregate initialiser */
if ((ident == POINTER || ident == VARIABLE) && type == STRUCT) {
/* aggregate is structure or pointer to structure */
dim = 0; olddim = 1;
if (ident == POINTER)
point();
str_init(tag);
} else {
/* aggregate is not struct or struct pointer */
agg_init(size, type, ident, &dim, more, tag);
}
needchar('}');
} else {
/* single initialiser */
init(size, ident, &dim, more, 0, 0);
}
/* dump literal queue and fill tail of array with zeros */
if ((ident == ARRAY && more == CCHAR) || type == STRUCT) {
if (type == STRUCT) {
dumpzero(tag->size, dim);
desize = dim < 0 ? abs(dim+1)*tag->size : olddim * tag->size;
} else { /* Handles unsized arrays of chars */
dumpzero(size, dim);
dim = dim < 0 ? abs(dim+1) : olddim;
cscale(type,tag,&dim);
desize = dim;
}
dumplits(0, YES, gltptr, glblab, glbq);
} else {
if (!(ident == POINTER && type == CCHAR)) {
dumplits(((size == 1) ? 0 : size), NO, gltptr, glblab,glbq);
if ( type != CCHAR ) /* Already dumped by init? */
desize = dumpzero(size, dim);
dim = dim < 0 ? abs(dim+1) : olddim;
cscale(type,tag,&dim);
desize = dim;
}
}
output_section("code_compiler"); // output_section("code");
} else {
char *dosign, *typ;
dosign = "";
if (ident == ARRAY && (dim == 0)) {
typ = ExpandType(more, &dosign, (tag - tagtab));
warning(W_NULLARRAY, dosign, typ);
}
/* no initialiser present, let loader insert zero */
if (ident == POINTER)
type = (zfar ? CPTR : CINT);
cscale(type, tag, &dim);
desize = dim;
}
return (desize);
}
