void normalisefastaUncompressed(libmaus::util::ArgInfo const & arginfo)
{
libmaus::fastx::StreamFastAReaderWrapper in(std::cin);
libmaus::fastx::StreamFastAReaderWrapper::pattern_type pattern;
unsigned int const cols = arginfo.getValue<unsigned int>("cols",getDefaultCols());
uint64_t offset = 0;
while ( in.getNextPatternUnlocked(pattern) )
{
std::string const name = pattern.getStringId();
std::string const shortname = stripName(name);
std::cerr << shortname << "\t" << pattern.patlen << "\t"
<< offset+pattern.getStringId().size()+2 << "\t" << cols << "\t" << cols+1 << std::endl;
pattern.printMultiLine(std::cout,cols,offset);
}
std::cout << std::flush;
}
void normalisefastaBgzf(libmaus::util::ArgInfo const & arginfo, std::ostream & out)
{
libmaus::fastx::StreamFastAReaderWrapper in(std::cin);
libmaus::fastx::StreamFastAReaderWrapper::pattern_type pattern;
int const level = libmaus::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue("level",getDefaultLevel()));
std::string const indexfn = arginfo.getUnparsedValue("index","");
::libmaus::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(level);
libmaus::lz::BgzfDeflate<std::ostream> defl(out,level,false /* full flush */);
uint64_t const inbufsize = defl.getInputBufferSize();
uint64_t zoffset = 0;
uint64_t ioffset = 0;
std::vector<libmaus::fastx::BgzfFastAIndexEntry> index;
std::ostringstream indexstr;
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,inbufsize);
uint64_t patid = 0;
while ( in.getNextPatternUnlocked(pattern) )
{
std::string const name = pattern.getStringId();
std::string const shortname = stripName(name);
std::string const & spat = pattern.spattern;
char const * cpat = spat.c_str();
uint64_t const patlen = spat.size();
uint64_t const numblocks = (patlen + inbufsize - 1)/inbufsize;
index.push_back(libmaus::fastx::BgzfFastAIndexEntry(shortname,patid++,ioffset));
ioffset += libmaus::util::StringSerialisation::serialiseString(indexstr,name);
ioffset += libmaus::util::StringSerialisation::serialiseString(indexstr,shortname);
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,patlen);
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,zoffset);
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,numblocks);
std::ostringstream nameostr;
nameostr << '>' << name << '\n';
std::string const nameser = nameostr.str();
std::pair<uint64_t,uint64_t> const P0 = defl.writeSyncedCount(nameser.c_str(),nameser.size());
zoffset += P0.second;
uint64_t o = 0;
while ( o != patlen )
{
assert ( o % inbufsize == 0 );
uint64_t const towrite = std::min(patlen-o,inbufsize);
std::pair<uint64_t,uint64_t> const P1 = defl.writeSyncedCount(cpat,towrite);
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,zoffset);
zoffset += P1.second;
o += towrite;
cpat += towrite;
}
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,zoffset);
std::pair<uint64_t,uint64_t> const Pn = defl.writeSyncedCount("\n",1);
zoffset += Pn.second;
}
defl.flush();
out << std::flush;
uint64_t const imetaoffset = ioffset;
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,index.size());
for ( uint64_t i = 0; i < index.size(); ++i )
ioffset += libmaus::util::NumberSerialisation::serialiseNumber(indexstr,index[i].ioffset);
libmaus::util::NumberSerialisation::serialiseNumber(indexstr,imetaoffset);
if ( indexfn.size() )
{
std::string const & sindex = indexstr.str();
libmaus::aio::CheckedOutputStream indexCOS(indexfn);
indexCOS.write(sindex.c_str(),sindex.size());
indexCOS.flush();
indexCOS.close();
}
}
void
xSpriteMan::addSpriteXms(std::string wname)
{
pugi::xml_document xms;
pugi::xml_node tex;
pugi::xml_node img;
std::string fname;
xSprite * a;
xTexture * skin;
unsigned int handle;
xAsset * w;
w = assetMan->getAsset(wname, ASSETGRP_XSPRITE);
if (w == 0) { printf("xSpriteMan -- asset doesnt exist %s \n", wname.c_str()); return; }
//todo -- check if file is zipped
fname = w->fname;
//dont clear, adds new sprite
if (!(xms.load_file(fname.c_str(), 0) )) { printf("xSpriteMan: Couldn't load xms [%s] \n", fname); return; }//endif
tex = xms.child("texture");
if (tex.empty() ) { return; } //todo error invalid file
float picw;
float pich;
std::string picname;
picw = (float) tex.attribute("width").as_int();
pich = (float) tex.attribute("height").as_int();
picname = tex.attribute("name").value();
handle = 0;
picname = stripName(picname);
skin = assetMan->getTexture(picname);
//skin = storeSkin.getData(picname);
if (skin == 0) { printf("xSpriteMan: image [%s] not loaded before sprites \n", picname.c_str()); }
else { handle = skin->handle; }
//todo -- refreshsprites instead? (go through all loaded sprites in a method or something)
for (img = tex.child("image"); img; img = img.next_sibling("image"))
{
a = new xSprite();
a->wname = img.attribute("name").value();
a->skin = picname;
a->handle = handle;
a->x = (float) img.attribute("x").as_int();
a->y = (float) img.attribute("y").as_int();
a->w = (float) img.attribute("width").as_int();
a->h = (float) img.attribute("height").as_int();
a->u0 = (float)(a->x) / picw;
a->v0 = (float)(a->y) / pich;
a->u1 = (float)(a->x + a->w) / picw;
a->v1 = (float)(a->y + a->h) / pich;
//printf("addsprite %s %0.2f %0.2f %u \n", a->wname.c_str(), a->x, a->y, a->handle);
storeSprite.addData(a->wname, a);
}//nextimg
}//addsprite
