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242 return "bam_data_source"

;

248 return "Bam Data Source"

;

265 if

(items.size() != 1 || workbench ==

) {

282

wxMenu* menu =

new

wxMenu;

283

menu->Append(wxID_SEPARATOR,

wxT

(

"Top Actions"

));

286

contrib.first = menu;

319 "attempt to open already open data source"

);

380 if

(obj.GetType().IsStr()) {

381 const string

& loader_type = obj.GetType().GetStr();

383 string

path,

, index, target_assm;

391 string msg

"Can't find the bam file: "

+ path +

;

395 if

(path + index).Exists()) {

396 string msg

"Can't find the bam index file: "

+ path + index;

406 if

( !target_assm.empty() ) {

417

loader_name =

.GetLoader()->GetName();

427 string msg

"Can't find the CSRA file: "

;

435

(*obj_mgr,

""

437

loader_name =

.GetLoader()->GetName();

447

loader_name =

.GetLoader()->GetName();

453

objects::CCSRADataLoader::TRegisterLoaderInfo

;

454 info

= objects::CCSRADataLoader::RegisterInObjectManager(*obj_mgr, sra,

456

loader_name =

.GetLoader()->GetName();

469 if

(obj.GetType().IsStr()) {

470 const string

& loader_type = obj.GetType().GetStr();

472 string

path,

, index, target_assm;

474

vector<CBAMDataLoader::SBamFileName> bam_files;

503 string

& path,

string

504 string

& idx,

string

& target_assm)

const 511 if

(field_path && field_file && field_index && field_target_assm) {

537 string

)

const 565

: m_Descr(

"Bam File data Loader"

""

)

569 wxT

(

"bam_data_source.png"

));

593 static string

ext_id(

"bam_data_source_type"

);

608

: m_SrvLocator(

609

m_ParentWindow(

612

m_OptionPanel(

613

m_IndexingPanel(

614

m_RefSequencesPanel(

615

m_GraphPanel(

616

m_ProjectSelPanel(

)

719 return

action ==

;

768 if

(action ==

) {

771

}

else if

(action ==

) {

779 if

(action ==

) {

786

}

else if

(action ==

) {

805 if

(action ==

) {

812

}

else if

(action ==

) {

819 if

(action ==

) {

822

}

else if

(action ==

) {

848

task->SetReportErrors(

false

);

855

bam_files.push_back(bam_input);

860

job->SetBamFiles(bam_files);

872 return

task.release();

900

list<string> input_list;

926

list<string> input_list;

928 if

(!input_list.empty()) {

947

unique_ptr<IIdMapper> idMapper;

948 if

(!mappedAcc.empty()) {

956 for

(

const auto

& itFile : files) {

957 CBamDb

db(mgr, itFile.first);

968 if

(added_ids.

insert

(id_str).second ==

true

) {

1002

vector<string> tokens;

1003 while

(getline(

, line)) {

1006 if

(tokens.size() < 4) {

1009 string

str_id = tokens[2];

1010 if

(str_id.empty()) {

1023 catch

(exception&) {

1032 m_Descr

"Loading BAM file"

;

1048 if

(i_str.length() < 4) {

1049

i_str.insert((

size_t

)0,

size_t

(4 - i_str.length()),

'0'

);

1051 return

sorted_file +

"."

+ i_str +

".bam"

;

1057 if

(i_str.length() < 4) {

1058

i_str.insert((

size_t

)0,

size_t

(4 - i_str.length()),

'0'

);

1060 return

sorted_file +

".tmp."

+ i_str +

".bam"

;

1067 if

((*iter)->IsName()) {

1068 return

(*iter)->GetName();

1096 string msg

(

"File format could not be determined:\n"

);

1103 string msg

"The graph file format is not supported!"

;

1104 msg

"\nGraph file: "

;

1115 string msg

"Can't deserialize the graph file. A seq-annot is expected. "

;

1117 msg

"\nGraph file: "

;

1122 string msg

"The input graph file doesn't cotain a graph!"

;

1123 msg

"\nGraph file: "

;

1129 msg

") needs to match with BAM file: "

+ annot_name;

1130 msg

"\nGraph file: "

;

1141 const string

& bam_file = iter->m_BamFile;

1142 LOG_POST

(

"Importing BAM file: "

<< bam_file);

1149 if

(iter->m_IndexFile.empty())

1160 LOG_POST

(

"Importing SRZ accession: "

<< *iter);

1165

loader->SetLabel(*iter);

1173

loader->SetData(*bam_data);

1188

loader->SetLabel(*iter);

1196

loader->SetData(*bam_data);

1206 LOG_POST

(

"Importing SRA accession: "

<< *iter);

1211

loader->SetLabel(*iter);

1219

loader->SetData(*bam_data);

1240 const string

& bam_file = bam_input.

m_BamFile

;

1241 if

(bam_file.empty()) {

1242 LOG_POST

(

Error

"CBamLoadingJob::x_CreateDataLoader(): " 1243 "Invalid (empty) bam file."

);

1251 if

(path.empty() ||

file_name

.empty()) {

1255 auto

GenerateIndex = [

this

](

const string

& bam_file,

const string

& index_file,

bool

generate_csi =

false

)

1266 while

(

proc

.IsAlive()) {

1269 CFile

t_file(index_file);

1279 catch

(exception&) {

1280 string msg

"Failed to generate the index file for "

+ bam_file;

1287 LOG_POST

(

"Generating BAI index file for "

<< bam_file);

1295 string

index_file = bam_file +

".bai"

;

1297 if

(!GenerateIndex(bam_file, index_file))

1301 if

(

(index_file).Exists())

1306 LOG_POST

(

"Generating CSI index file for "

<< bam_file);

1309 string

index_file = bam_file +

".csi"

;

1311 if

(!GenerateIndex(bam_file, index_file,

true

))

1316 if

(

(index_file).Exists())

1319 LOG_POST

(

Warning

"Maybe the input Bam file is not sorted. Try sorting it and do indexing again ..."

);

1335 while

(sort_proc.

IsAlive

()) {

1340 while

(file_i < 10000 &&

(t_file).Exists()) {

1347

sort_proc.

Wait

(2000);

1350 catch

(exception&) {

1351 string msg

"Failed to sort the BAM file: "

+ bam_file;

1358

sorted_file +=

".bam"

;

1360 if

(sorted_file).Exists()) {

1373 while

(sort_proc.

IsAlive

()) {

1378 while

(file_i < 10000 &&

(t_file).Exists()) {

1385

sort_proc.

Wait

(2000);

1388 catch

(exception&) {

1389 string msg

"Failed to sort the BAM file: "

+ bam_file;

1396 if

(

(sorted_file).Exists()) {

1400

index_file = sorted_file +

".bai"

;

1401 if

(!GenerateIndex(sorted_file, index_file))

1404 if

(

(index_file).Exists()) {

1411

index_file = sorted_file +

".csi"

;

1412 if

(!GenerateIndex(sorted_file, index_file,

true

))

1415 if

(