int samtools_main(int argc, char *argv[])
{
#ifdef _WIN32
setmode(fileno(stdout), O_BINARY);
setmode(fileno(stdin), O_BINARY);
#endif
if (argc < 2) { usage(pysamerr); return 1; }
if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
if (argc == 2) { usage(stdout); return 0; }
// Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
// main_xyz() functions by convention display the subcommand's usage
// when invoked without any arguments.
argv++;
argc = 2;
}
int ret = 0;
if (strcmp(argv[1], "view") == 0) ret = main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) ret = main_import(argc-1, argv+1);
else if (strcmp(argv[1], "mpileup") == 0) ret = bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) ret = bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) ret = bam_sort(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bam_index(argc-1, argv+1);
else if (strcmp(argv[1], "idxstats") == 0) ret = bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) ret = faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "dict") == 0) ret = dict_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) ret = bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) ret = bam_rmdup(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) ret = bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "reheader") == 0) ret = main_reheader(argc-1, argv+1);
else if (strcmp(argv[1], "cat") == 0) ret = main_cat(argc-1, argv+1);
else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
else if (strcmp(argv[1], "phase") == 0) ret = main_phase(argc-1, argv+1);
else if (strcmp(argv[1], "depth") == 0) ret = main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0 ||
strcmp(argv[1], "fastq") == 0 ||
strcmp(argv[1], "fasta") == 0) ret = main_bam2fq(argc-1, argv+1);
else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "depad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "bedcov") == 0) ret = main_bedcov(argc-1, argv+1);
else if (strcmp(argv[1], "bamshuf") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "collate") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "stats") == 0) ret = main_stats(argc-1, argv+1);
else if (strcmp(argv[1], "flags") == 0) ret = main_flags(argc-1, argv+1);
else if (strcmp(argv[1], "split") == 0) ret = main_split(argc-1, argv+1);
else if (strcmp(argv[1], "quickcheck") == 0) ret = main_quickcheck(argc-1, argv+1);
else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(pysamerr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
}
else if (strcmp(argv[1], "tview") == 0) ret = bam_tview_main(argc-1, argv+1);
else if (strcmp(argv[1], "--version") == 0) {
printf(
"samtools %s\n"
"Using htslib %s\n"
"Copyright (C) 2015 Genome Research Ltd.\n",
samtools_version(), hts_version());
}
else if (strcmp(argv[1], "--version-only") == 0) {
printf("%s+htslib-%s\n", samtools_version(), hts_version());
}
else {
fprintf(pysamerr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
return ret;
}
void c_FeatureReaderToHtml::ToTemplate(bool IsKml,c_RestDataReader* Reader, c_RestRequest* RestRequest
, const string& FullUri,const string& UriBase
,string& HtmlStr,int StartIndex,int MaxCount)
{
Ptr<MgClassDefinition> classdef;
// classdef = if( FeatureReader ) FeatureReader->GetClassDefinition() ;
classdef = RestRequest->m_DataClassDef;
if( !classdef ) return;
//const c_CfgDataLayer* cfgdata = MgRest_MapNameToResourceId::GetCfgDataForClass(classfullname);
const c_CfgDataResource* cfgresource = RestRequest->m_CfgDataResource;
if( !cfgresource ) return; // error ; class has to be in configuration file
const c_CfgRepTemplate* templatedata;
if( RestRequest->m_CfgRepresentation->GetType() != c_CfgRepresentation::e_Template )
{
return;
}
templatedata = (c_CfgRepTemplate*)RestRequest->m_CfgRepresentation;
string rest_uri_part;
if( cfgresource->m_RestUriPart.length() > 0 )
{
MgUtil::WideCharToMultiByte(cfgresource->m_RestUriPart,rest_uri_part);
}
else
{
rest_uri_part = "/rest/data/";
}
//ctemplate::Template::SetTemplateRootDirectory(g_HtmlTemplatePath);
ctemplate::Template::SetTemplateRootDirectory(RestRequest->m_CfgDataResource->m_TemplateFolder);
// get identity property name;
STRING identname;
if( classdef )
{
Ptr<MgPropertyDefinitionCollection> idents = classdef->GetIdentityProperties();
if( idents->GetCount() == 1)
{
int ind=0;
Ptr<MgPropertyDefinition> identprop = idents->GetItem(ind);
identname = identprop->GetName();
}
else
{
identname = L"";
}
}
ctemplate::TemplateDictionary dict_main("KING.MGREST");
// now fill in request parameters
if( RestRequest )
{
Ptr<c_RestUriRequestParam> req_param = RestRequest->GetRequestParam();
MgStringPropertyCollection* params = req_param->GetParameters();
if( params && (params->GetCount()>0) )
{
string dictkey;
string param_name,param_val;
string keyprefix = "REST_PARAM_";
for(int ind=0;ind<params->GetCount();ind++)
{
Ptr<MgStringProperty> param = params->GetItem(ind);
MgUtil::WideCharToMultiByte(param->GetName(),param_name);
ReplaceSpaces(param_name); // google ctemplate doesn't allow spaces
MgUtil::WideCharToMultiByte(param->GetValue(),param_val);
dict_main.SetValue(keyprefix+param_name,param_val);
}
}
}
string resturiparam;
bool ismorerecords=false;
int featurecount=0;
if( (classdef != NULL) && (Reader!=NULL) )
{
STRING wresturiparam = cfgresource->m_UriTag;
MgUtil::WideCharToMultiByte(wresturiparam,resturiparam);
bool isnext=true;
int skipstart = StartIndex;
if( skipstart > 0 )
{
while ( (skipstart>0) && (isnext=Reader->ReadNext())==true )
{
skipstart--;
}
}
if( isnext )
{
string dictname; // = mb_classname;
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Section,dictname);
string nameprefix; // = mb_classname + "_";
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Prefix,nameprefix);
while ( Reader->ReadNext() )
{
if( MaxCount >= 0 )
{
if( featurecount >= MaxCount )
{
ismorerecords=true;
break; // go out
}
}
ctemplate::TemplateDictionary* dict_section = dict_main.AddSectionDictionary(dictname);
FillDictionary(dict_section,nameprefix,Reader);
if( identname.length() > 0 )
{
STRING strval;
string mb_strval;
GetPropertyAsString(Reader,identname,strval);
MgUtil::WideCharToMultiByte(strval,mb_strval);
//
string dictkey = nameprefix + "REST_PNG";
string val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".png";
dict_section->SetValue(dictkey,val);
dictkey = nameprefix + "REST_HTML";
val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".html";
dict_section->SetValue(dictkey,val);
dictkey = nameprefix + "REST_KML";
val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".kml";
dict_section->SetValue(dictkey,val);
dictkey = nameprefix + "REST_KMZ";
val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".kmz";
dict_section->SetValue(dictkey,val);
dictkey = nameprefix + "REST_XML";
val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".xml";
dict_section->SetValue(dictkey,val);
dictkey = nameprefix + "REST_JSON";
val = UriBase + rest_uri_part + resturiparam + "/" + mb_strval + ".json";
dict_section->SetValue(dictkey,val);
// create feature identifier value as base64 coded
string ident_base64;
GetPropertyAsBase64(Reader,identname,ident_base64);
dictkey = nameprefix + "REST_IDENT_BASE64";
dict_section->SetValue(dictkey,ident_base64);
}
featurecount++;
}
}
// Now check additional data to be fetched for html template
// it applies only to single feature templates
if( featurecount==1 && templatedata->GetCountHtmlExtraData() > 0 )
{
int count = templatedata->GetCountHtmlExtraData();
for(int ind=0;ind<count;ind++)
{
const c_CfgRepTemplateExtraData* extradata = templatedata->GetHtmlExtraData(ind);
if( extradata->m_FetchUri.length() > 0 )
{
// generate template unique name
std::string filename,mb_str;
MgUtil::WideCharToMultiByte(cfgresource->m_UriTag,filename);
MgUtil::WideCharToMultiByte(extradata->m_HtmlTemp_Prefix,mb_str);
filename += mb_str;
MgUtil::WideCharToMultiByte(extradata->m_FetchUri,mb_str);
filename="";
ctemplate::Template * temp = ctemplate::Template::StringToTemplate(mb_str,ctemplate::STRIP_WHITESPACE);
/*
ctemplate::Template * temp = ctemplate::Template::RegisterStringAsTemplate(filename,
ctemplate::STRIP_WHITESPACE,ctemplate::TC_MANUAL,mb_str);
*/
std::string uristr;
temp->Expand(&uristr,&dict_main);
// Now use uristr to fetch data
std::string mb_str2,mb_str3,mb_str4;
MgUtil::WideCharToMultiByte(extradata->m_HtmlTemp_Section,mb_str2);
MgUtil::WideCharToMultiByte(extradata->m_HtmlTemp_DataSection,mb_str3);
MgUtil::WideCharToMultiByte(extradata->m_HtmlTemp_Prefix,mb_str4);
c_RestFetchSource::FetchFeaturesToDictionary( uristr,&dict_main,mb_str2,mb_str3,mb_str4 );
delete temp;
}
}
}
// now add in dictionary values for next and previous
if( ismorerecords || StartIndex>0 )
{
Poco::URI uri_parser(FullUri);
std::string query = uri_parser.getQuery();
c_RestUriRequestParam params;
c_RestUri::ParseQuery(query.c_str(),¶ms);
if( StartIndex>0 )
{
int newstart = StartIndex - MaxCount;
if( newstart < 0 ) newstart=0;
newstart++;
wchar_t strstart[20];
::swprintf(&strstart[0],L"%d",newstart);
if( params.ContainsParameter(L"Start") )
{
params.SetParameterValue(L"Start",strstart);
}
else
{
params.AddParameter(L"Start",strstart);
}
wstring wuriquery;
params.GetAsUriQuery(wuriquery);
string uriquery;
MgUtil::WideCharToMultiByte(wuriquery,uriquery);
//string prev_uri = UriBase + rest_uri_part + resturiparam + "/" + ".html" + "?" + uriquery;
string prev_uri = "?" + uriquery; // use only query part so link will be correct in case of url rewrites
ctemplate::TemplateDictionary* dict_section = dict_main.AddSectionDictionary("PREVIOUS_PAGE_SECTION");
string dictkey = "PREVIOUS_PAGE";
dict_section->SetValue(dictkey,prev_uri);
}
else
{
// no previous link
//string dictkey = nameprefix + "PREVIOUS_PAGE";
//dict_main.SetEscapedValue(,);
}
if( ismorerecords>0 )
{
int newstart = StartIndex + MaxCount;
if( newstart < 0 ) newstart=0;
newstart++;
wchar_t strstart[20];
::swprintf(&strstart[0],L"%d",newstart);
if( params.ContainsParameter(L"Start") )
{
params.SetParameterValue(L"Start",strstart);
}
else
{
params.AddParameter(L"Start",strstart);
}
wstring wuriquery;
params.GetAsUriQuery(wuriquery);
string uriquery;
MgUtil::WideCharToMultiByte(wuriquery,uriquery);
//string next_uri = UriBase + rest_uri_part + resturiparam + "/" + ".html" + "?" + uriquery;
string next_uri = "?" + uriquery; // use only query part so link will be correct in case of url rewrites
ctemplate::TemplateDictionary* dict_section = dict_main.AddSectionDictionary("NEXT_PAGE_SECTION");
string dictkey = "NEXT_PAGE";
dict_section->SetValue(dictkey,next_uri);
}
else
{
// no previous link
//string dictkey = nameprefix + "NEXT_PAGE";
//dict_main.SetEscapedValue(,);
}
}
}
string tmpl; // name of template to use
if(Reader)
{
if( featurecount == 1 )
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Single,tmpl);
else
{
if( featurecount == 0 )
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Zero,tmpl);
else
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Many,tmpl);
}
}
else
{
// if there was no feature reader
MgUtil::WideCharToMultiByte(templatedata->m_HtmlTemp_Error,tmpl);
if(RestRequest->m_RestResultObjectStatus == c_RestRequest::e_BBox_OutOfRange )
dict_main.ShowSection("EXCEPTION_BBOX_LIMIT");
if(RestRequest->m_RestResultObjectStatus == c_RestRequest::e_Count_OutOfRange )
dict_main.ShowSection("EXCEPTION_COUNT_LIMIT");
}
/*
string tmpl = mb_classname;
// if there is only one feature then use different template
// name of that template for class "parcel" is parcel.tpl , added "1" to end of class name
if( count <= 1 )
{
tmpl.append("1");
}
tmpl.append(".tpl");
*/
ctemplate::Template::ReloadAllIfChanged();
ctemplate::TemplateContext tc;
if( IsKml )
tc = ctemplate::TC_XML;
else
tc = ctemplate::TC_HTML;
//ctemplate::Template* tpl = ctemplate::Template::GetTemplateWithAutoEscaping(tmpl,ctemplate::DO_NOT_STRIP,tc);
ctemplate::Template* tpl = ctemplate::Template::GetTemplate(tmpl,ctemplate::DO_NOT_STRIP);
if( !tpl )
{
//Ptr<MgStringCollection> scol = new MgStringCollection();
std::wstring wsarg;
MgUtil::MultiByteToWideChar(tmpl,wsarg);
//scol->Add(wsarg);
std::wstring errmsg = L"Unable to load Template file '";
errmsg = errmsg.append(wsarg);
errmsg = errmsg.append(L"'. Check config file and template file location!");
throw new MgRuntimeException(L"c_FeatureReaderToHtml::ToTemplate",__LINE__, __WFILE__, NULL, errmsg, NULL);
}
tpl->Expand(&HtmlStr,&dict_main);
}//end of c_FeatureReaderToHtml::ToTemplate
