bool within_mvt(char fc, int fr, char tc, int tr, int stepc, int stepr, bool multistep, int mvmt)
{
/*
fc - from-column A-H
fr - from-row 1-8
stepc - mvt per step in column
stepr - mvt per step in row
multistep - just move once, or keep moving until finding obstacles
*/
bool is_capture = iscol(fc, fr, true) != iscol(tc, tr, true);
if ((is_capture && !(mvmt&CAPT)) ||
(!is_capture && !(mvmt&MOVE)))
return false;
while ((fc >= 'A' && fc <= 'H' && fr >= 1 && fr <= 8) && (tc >= 'A' && tc <= 'H' && tr >= 1 && tr <= 8))
{
fc += stepc;
fr += stepr;
if (fc == tc && fr == tr)
{
return CBD(tc, tr) == EMP || is_capture;
}
if (CBD(fc, fr) != EMP)
{
break;
}
if (!multistep)
{
break;
}
}
return false;
}
static unsigned int Call(Args&&... args) {
constexpr ScriptCallbackData const& data = CBD(I);
static_assert(data.callback.matches(TypeString<typename std::remove_reference<Args>::type...>::value), "Wrong number or types of arguments");
unsigned int count = 0;
for (auto& script : scripts)
{
if (!script->callbacks_.count(I))
script->callbacks_.emplace(I, script->GetScript<FunctionEllipsis<void>>(data.name));
auto callback = script->callbacks_[I];
if (!callback)
continue;
if (script->cpp_script)
reinterpret_cast<FunctionEllipsis<CBR<I>>>(callback)(std::forward<Args>(args)...);
else
PAWN::Call(script->amx, data.name, data.callback.types, B, std::forward<Args>(args)...);
++count;
}
return count;
}
void create_spin_degrees(int direction, int degrees, int speed) {
speed = (int) (speed * MILLIMETERS_PER_DEGREE);
create_spin(speed, direction);
_wait_degrees(direction * degrees);
create_halt();
CBD();
}
void create_drive_distance(int direction, float centimeters, float speed) {
float overshoot = (.1 * speed) - 1;
int millimeters = (int) ((centimeters - overshoot) * 10);
create_drive_OI(speed * 10, direction);
_wait_distance((millimeters * direction) - overshoot);
create_halt();
CBD();
}
int make_move(char fc, int fr, char tc, int tr)
{
fc = toupper(fc);
tc = toupper(tc);
if (fc<'A' || fc>'H' || tc<'A' || tc>'H' || fr > 8 || fr < 1 || tr>8 || tr < 1)
{
return MV_INVALID;
}
int mv_type = get_move_type(fc, fr, tc, tr);
if (mv_type == MT_MOVE)
{
CBD(tc, tr) = CBD(fc, fr);
CBD(fc, fr) = EMP;
white_turn = !white_turn;
return MV_OK;
}
else if (mv_type == MT_CASTLE_SRT || mv_type == MT_CASTLE_LNG)
{
char rook_from = mv_type == MT_CASTLE_LNG ? 'A' : 'H',
rook_to = mv_type == MT_CASTLE_LNG ? 'D' : 'F';
int op_row = white_turn ? 1 : 8;
CBD(tc, tr) = CBD(fc, fr);
CBD(fc, fr) = EMP;
//move the rook!
CBD(rook_to, op_row) = CBD(rook_from, op_row);
CBD(rook_from, op_row) = EMP;
if (white_turn)
{
white_can_castle_long = white_can_castle_short = false;
}
else
{
black_can_castle_long = black_can_castle_short = false;
}
white_turn = !white_turn;
return MV_OK;
}
return MV_ILLEGAL;
}
int get_move_type(char fc, int fr, char tc, int tr)
{
if ((iscol(fc, fr, true) && iscol(tc, tr, true)) || (iscol(fc, fr, false) && iscol(tc, tr, false)))
{
return false;
}
if (!iscol(fc, fr, white_turn)) return false;
switch (toupper(CBD(fc, fr)))
{
case 'P':
//emp check
//cap chk
break;
case 'N':
return KNCHK ? MT_MOVE : MT_ILLEGAL;
break;
case 'B':
return BSCHK ? MT_MOVE : MT_ILLEGAL;
break;
case 'R':
return RKCHK ? MT_MOVE : MT_ILLEGAL;
break;
case 'Q':
return QNCHK ? MT_MOVE : MT_ILLEGAL;
break;
case 'K':
if (KGCHK)
return MT_MOVE;
if (castle_check(fc, fr, tc, tr, white_turn))
{
return tc == 'G' ? MT_CASTLE_SRT : MT_CASTLE_LNG;
}
break;
case ' ':
return MT_ILLEGAL;
default:
return MT_ILLEGAL;
}
return MT_MOVE;
}
int bamfixmatecoordinates(::libmaus::util::ArgInfo const & arginfo)
{
::libmaus::util::TempFileRemovalContainer::setup();
::libmaus::timing::RealTimeClock rtc; rtc.start();
bool const verbose = arginfo.getValue<unsigned int>("verbose",getDefaultVerbose());
unsigned int const colhashbits = arginfo.getValue<unsigned int>("colhashbits",getDefaultColHashBits());
unsigned int const collistsize = arginfo.getValue<unsigned int>("collistsize",getDefaultColListSize());
int const level = arginfo.getValue<int>("level",getDefaultLevel());
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
switch ( level )
{
case Z_NO_COMPRESSION:
case Z_BEST_SPEED:
case Z_BEST_COMPRESSION:
case Z_DEFAULT_COMPRESSION:
break;
default:
{
::libmaus::exception::LibMausException se;
se.getStream()
<< "Unknown compression level, please use"
<< " level=" << Z_DEFAULT_COMPRESSION << " (default) or"
<< " level=" << Z_BEST_SPEED << " (fast) or"
<< " level=" << Z_BEST_COMPRESSION << " (best) or"
<< " level=" << Z_NO_COMPRESSION << " (no compression)" << std::endl;
se.finish();
throw se;
}
break;
}
std::string const tmpfilename = tmpfilenamebase + "_bamcollate";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfilename);
::libmaus::bambam::CollatingBamDecoder CBD(std::cin,tmpfilename,false /* put rank */,colhashbits/*hash bits*/,collistsize/*size of output list*/);
::libmaus::bambam::BamFormatAuxiliary auxdata;
::libmaus::bambam::BamHeader const & bamheader = CBD.getHeader();
// add PG line to header
std::string const upheadtext = ::libmaus::bambam::ProgramHeaderLineSet::addProgramLine(
bamheader.text,
"bamfixmatecoordinates", // ID
"bamfixmatecoordinates", // PN
arginfo.commandline, // CL
::libmaus::bambam::ProgramHeaderLineSet(bamheader.text).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
::libmaus::bambam::BamHeader uphead(upheadtext);
if ( uphead.getSortOrder() != "queryname" )
uphead.changeSortOrder("unknown");
/*
* start index/md5 callbacks
*/
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
// setup bam writer
::libmaus::bambam::BamWriter::unique_ptr_type writer(new ::libmaus::bambam::BamWriter(std::cout,uphead,level,Pcbs));
#if 0
::libmaus::bambam::ProgramHeaderLineSet PHLS(bamheader.text);
std::cerr << "Last id in PG chain: " << PHLS.getLastIdInChain() << std::endl;
#endif
// std::cout << bamheader.text;
typedef ::libmaus::bambam::CollatingBamDecoder::alignment_ptr_type alignment_ptr_type;
std::pair<alignment_ptr_type,alignment_ptr_type> P;
uint64_t const mod = 1024*1024;
uint64_t proc = 0;
uint64_t lastproc = 0;
uint64_t paircnt = 0;
while ( CBD.tryPair(P) )
{
uint64_t const mapcnt = getMapCnt(P.first) + getMapCnt(P.second);
if ( mapcnt == 1 )
{
int32_t refid = -1;
int32_t pos = -1;
if ( P.first )
{
refid = P.first->getRefID();
pos = P.first->getPos();
}
else
{
assert ( P.second );
refid = P.second->getRefID();
pos = P.second->getPos();
}
P.first->putRefId(refid);
P.first->putPos(pos);
P.first->putNextRefId(refid);
P.first->putNextPos(pos);
P.second->putRefId(refid);
P.second->putPos(pos);
P.second->putNextRefId(refid);
P.second->putNextPos(pos);
}
if ( P.first )
{
P.first->serialise(writer->getStream());
++proc;
}
if ( P.second )
{
P.second->serialise(writer->getStream());
++proc;
}
if ( P.first && P.second )
{
paircnt++;
}
if ( verbose && (proc/mod != lastproc/mod) )
{
std::cerr
<< "Processed " << proc << " fragments, " << paircnt << " pairs, "
<< proc/rtc.getElapsedSeconds() << " al/s"
<< std::endl;
lastproc = proc;
}
}
if ( verbose )
std::cerr
<< "Processed " << proc << " fragments, " << paircnt << " pairs, "
<< proc/rtc.getElapsedSeconds() << " al/s"
<< std::endl;
writer.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return EXIT_SUCCESS;
}
static constexpr ScriptCallbackData const& CBD(const unsigned int I, const unsigned int N = 0) {
return callbacks[N].index == I ? callbacks[N] : CBD(I, N + 1);
}
