sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2e588e6838b2bfbb46e94c00b6ed6b891b55e67c66ad4c3cf08baf450930e9cd | C++ | 18,580 | 390 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
78d082b7472523679c9e8f084b5079b298f2805fa0bf568eb861d37c7b05d4e9 | C++ | 18,693 | 504 | /// \file unittest/aligner.cpp
///
/// Unit tests for the basic methods of the Aligner class. See also:
/// pinned_alignment.cpp.
///
#include <iostream>
#include <string>
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include "vg.hpp"
#include "path.hpp"
#include "support/test_aligner.hpp"
#include "catch.hpp"
... |
c751c6dcd65129885364b9d4d333e1b999506defb03a2a648ca38211cd1a3708 | C++ | 18,746 | 486 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
b4f369c293b242883ae5c63fc5dd2af9aaaa7047730fb8bd8bd34aae47d20bd0 | C++ | 18,815 | 520 | /** \file
* Implements per-component algorithms
*/
#include <queue>
#include <thread>
#include <atomic>
#include <mutex>
#include <structures/union_find.hpp>
#include "../cluster.hpp"
#include "component.hpp"
#include "utility.hpp"
#include "sdsl/bit_vectors.hpp"
#include "sdsl/int_vector.hpp"
//#define debug_comp... |
a40ac88edf56e36e56b92554c17b444ccfbab204a3f4d5bdc137291f1d1875ea | C++ | 18,875 | 634 | //! \file us_dcdt.cpp
#include <QApplication>
#include <QtSvg>
#include "us_dcdt.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
//! \brief Main program for us_dcdt. Loads translators and starts
// the class US_Dcdt.
int mai... |
60a60c93d39f5898a342e1afc806160fbfdb8d1093443afc0ef2dca4e78679d9 | C++ | 18,952 | 587 | // Reject malformed AUC files, including mutations with valid checksums.
#include "qt_test_base.h"
#include "us_crc.h"
#include "us_dataIO.h"
#include <QByteArray>
#include <QElapsedTimer>
#include <QFile>
#include <QTemporaryDir>
#include <QtEndian>
namespace
{
// Fixed header layout, from writeRawData():
// 0 ... |
7f2867caed27c05ea17878be305f0bd3ec517c347c7d47fdf841fa10cf7cbe9e | C++ | 19,012 | 435 | #include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <set>
#include "vg/io/json2pb.h"
#include "../vg.hpp"
#include "../xg.hpp"
#include "catch.hpp"
#include "../snarls.hpp"
#include "../cactus_snarl_finder.hpp"
#include "../integrated_snarl_finder.hpp"
#include "../cluster.hpp"
#inclu... |
ba6cb177bca6fa759bd6a127e03d71a77945323e6e63875cebd14ba8d8a55503 | C++ | 19,119 | 711 | #include <cmath>
#include <iostream>
#include <limits>
#include <numeric>
#include <set>
#include <vector>
#include <graphtyper/graph/graph.hpp> // gyper::Graph
#include <graphtyper/utilities/graph_help_functions.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/options.hpp> // *gyper::Op... |
c8e0079bf6b3f80e4e26f05b4e6153ffbc2e597bce6bb7c1aa9eb591c83d4e7c | C++ | 19,255 | 396 | // tests_unit.cpp -- synthetic-geometry unit tests for the perceiver.
#include <sstream>
#include <string>
#include <vector>
#include "../tinytest.h"
#include "../../include/us_hydrodyn_perceive.h"
#include "../../include/us_hydrodyn_perceive_hybrid.h"
#include "../../include/us_hydrodyn_perceive_elements.h"
using nam... |
06bb4b915aa0124e39ae9763d566dfb7d77d6c8f9da121d87652fc9ec0f8968c | C++ | 19,296 | 453 | /**
* \file min_cut_graph.cpp
*
* Contains implementation of min_cut_graph function
*/
#include "min_cut_graph.hpp"
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <structures/union_find.hpp>
#include "../contracting_graph.hpp"
#include <random>
#include <iostream>
#include <algorithm>
#include ... |
f45748539e0883dfa5c3fffec25016852ae910099d041e06b0c427933b59658a | C++ | 19,305 | 586 | #include "us_mpi_analysis.h"
#include "us_util.h"
#include "us_math2.h"
#include "us_settings.h"
void US_MPI_Analysis::ga_master( void )
{
current_dataset = 0;
datasets_to_process = count_datasets;
max_depth = 0;
calculated_solutes.clear();
// Set noise and debug flags
simulation_value... |
f7d2c88c85a42145014b9ba58ef566cf0ee740265524b9b34e516b1a04fc08ce | C++ | 19,461 | 604 | //! \file us_dmga_init.cpp
#include <QApplication>
#include "us_dmga_init.h"
#include "us_constraints_edit.h"
#include "us_model_loader.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_math2.h"
#include "us_matrix.h"
#include "us_constants.h"
#inc... |
95a6c454fdd3d6a1dde0ac1d818c0129007c3e476aa2c4fa3dfa69805dc091b1 | C++ | 19,464 | 488 | // snarl_main.cpp: define the "vg snarls" subcommand, which outputs snarls and bubbles
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include <regex>
#include "subcommand.hpp"
#include "../vg.hpp"
#include <vg/vg.pb.h>
#include "../traversal_finder.hpp"
#include "../cac... |
fbe451d4a0d753cd668091b6b67f83063995eade6c039c79a36451d4643f88b5 | C++ | 19,543 | 471 | #include "mcmc_caller.hpp"
#include "graph_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "memoizing_graph.hpp"
#include "phased_genome.hpp"
// #define debug
namespace vg {
/**
* MCMCCaller : Inherits from VCFOutputCaller
*/
MCMCCaller::MCMCCaller(const PathPositionHand... |
a39c37458b308d5c3326a6a051efbd4974ac75490d918583c7c023f7a305c329 | C++ | 19,670 | 599 | //! \file test_us_dataIO_roundtrip.cpp
// AUC round trips, format precision, and writer validation.
#include "qt_test_base.h"
#include "us_dataIO.h"
#include "us_settings.h"
#include <QByteArray>
#include <QFile>
#include <QTemporaryDir>
#if defined(Q_OS_UNIX) && GTEST_HAS_DEATH_TEST
#include <csignal>
#include <cst... |
7f0b660c5fb3779efd21011c5fd3b4ced2c3ca78dfb7a6ed1d8ba0104ca9501c | C++ | 19,815 | 408 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
a2fea653bdcae6c7e2ddc8a959ccca314c794384091175129c33d97a3a75da88 | C++ | 19,844 | 699 | //! \file us_fit_worker.cpp
#include "us_fit_worker.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_sleep.h"
#include <cfloat>
const double dflt_min = (double)FLT_MIN;
const double dflt_max = (double)FLT_MAX;
// Construct fit worker thread
US_FitWorker::US_FitWorker( US_EqMath* emath, FitCtrl... |
48f8c3984b14800d60825af91e287860679575a4cc8e04e089259e943cb5c230 | C++ | 19,928 | 617 | /**
* \file
* unittest/variant_adder.cpp: test cases for the add-variants-to-existing-graph tool
*/
#include "catch.hpp"
#include "../variant_adder.hpp"
#include "../handle.hpp"
#include "../utility.hpp"
#include "../path.hpp"
#include "../io/json2graph.hpp"
#include <vector>
#include <sstream>
#include <iostrea... |
d7024a9bdc72b49d88463e13ca9843ce643b0098d3525b1dbd8237b3503ab3df | C++ | 19,993 | 432 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
0c0513d27da932f8655c9be340c5d99d36ed034ddf5650ebf9f02f84ef23ccb4 | C++ | 20,081 | 457 | #include "subcommand.hpp"
#include "../vg.hpp"
#include "../utility.hpp"
#include "../integrated_snarl_finder.hpp"
#include "../io/save_handle_graph.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <vg/io/alignment_emitter.hpp>
#include "../clip.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
#incl... |
214bb8fab4deb396145dd0202b67521e7fa63179c714d1facacf29f860f29fa4 | C++ | 20,153 | 504 | // gamcompare_main.cpp: defines a GAM to GAM annotation function
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <string>
#include <vector>
#include <set>
#include <iomanip>
#include "subcommand.hpp"
#include "../alignment.hpp"
#include "../annotation.hpp"
#include "../snarl_distance_index.hpp"
#i... |
87c1c33109d5ccd2210d3c8ca9c365c72c50d047e6fe6260caa6fd0f9e476da8 | C++ | 20,161 | 548 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
b08e9c409404f215b13e04305a153a28e60bebedb3cd94132c5f4a5d49fc7005 | C++ | 20,218 | 441 | #include "mapping_quality_calculator.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <limits>
#include "alignment.hpp"
#include "statistics.hpp"
namespace vg {
using std::log;
using std::log10;
using std::max;
using std::min;
using std::pair;
using std::pow;
using std::round;
using std::sqrt;... |
3e2960ac514a4e17a76fc43edd830314a16474e2cca4c37879b8297072af51be | C++ | 20,270 | 361 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
9da1a3de0f75e73b6e190c57b48819682c6c2ba36a35acb667bb356304c35c56 | C++ | 20,461 | 559 | #include <cstdio>
#include <fstream>
#include <iostream>
#include <string>
#include <sys/stat.h>
#include <sys/types.h>
#include <vector>
#include <cereal/archives/binary.hpp>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/gra... |
942c53799c8b4c66afddcc918e87f0edef6ea948a6bc1bd206677eefc18a33ea | C++ | 20,490 | 577 | #include "us_legacy_converter.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_archive.h"
int main(int argc, char *argv[])
{
QApplication application(argc, argv);
#include "main1.inc"
// License is OK. Start up.
US_LegacyConverter* w = new US_LegacyConverter;
w->show(); ... |
18ac919ff6fc711eab480f0f7b5373a62b9f510e87bc19e78257cdc34ca7265b | C++ | 20,520 | 517 | /// \file dagify.cpp
///
/// unit tests for the handle based dagify algorithm
///
#include <iostream>
#include "vg/io/json2pb.h"
#include "../vg.hpp"
#include "../split_strand_graph.hpp"
#include "support/random_graph.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
#include "handlegraph/algorithms/find_ti... |
ba202eb51ae0a1d496777bbd6de46a17b304d0a044a973d5c658790572fc0ce6 | C++ | 20,522 | 439 | #include "coverage_depth.hpp"
#include <bdsg/hash_graph.hpp>
#include "algorithms/subgraph.hpp"
#include <vg/io/stream.hpp>
#include "../path.hpp"
namespace vg {
namespace algorithms {
// Senses included when counting path steps for coverage. HAPLOTYPE is
// included so haplotype paths stored in GBZ/GBWT contribute ... |
3e122e226dc53f446d55dfd9272909c66773d6188fb779fe679dad4c63dd858a | C++ | 20,644 | 591 | #include "us_gui_settings.h"
#include "us_theme.h"
#include "us_defines.h"
#include "us_settings.h"
namespace
{
//! One entry of a palette color table
struct RoleColor
{
QPalette::ColorRole role;
QColor color;
};
//! Apply a role/color table to the Active and Inactive groups of... |
9516da18dde8021250a413874f14c3b54e8fc22280257addf640e6a33e93af9a | C++ | 20,655 | 491 | /**
* \file multipath_alignment_emitter.cpp
*
* Implements a system for emitting multipath alignments and groups of multipath alignments in multiple formats.
*/
#include "multipath_alignment_emitter.hpp"
#include "vg/io/json2pb.h"
using namespace vg::io;
namespace vg {
using namespace std;
MultipathAlignmentEmi... |
4230f192b26701823748641f4b89929cc107c8bca48bd826cf449330c47a9b50 | C++ | 20,705 | 667 | //! \file us_load_run_noise.cpp
#include <QtGui>
#include "us_load_run_noise.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_util.h"
#include "us_investigator.h"
// Constructor
US_LoadRunNoise::US_LoadRunNoise( QObject* p... |
9e73f2462d1c6396f4fa81dedf0983054b3726d1de56d82991596f9a74fe46d3 | C++ | 20,729 | 728 | //! \file us_extinctfitter_gui.cpp
#include "us_extinctfitter_gui.h"
#include "us_gui_util.h"
US_ExtinctFitter::US_ExtinctFitter(QVector <struct WavelengthScan> *temp_wls_v, double*& temp_guess, unsigned int& temp_order, unsigned int& temp_parameters, QString& temp_projectName, bool *temp_fitting_widget) : US_Minimi... |
ac83d9b6b7293587e751152e49cbbdaa059c16976f83bb6b678ba318a7e900e7 | C++ | 20,791 | 472 | /** \file deconstruct_main.cpp
*
* Defines the "vg deconstruct" subcommand, which turns graphs back into VCFs.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../deconstructor.hpp"
#include "../gref.hpp"
#include "../integr... |
e03ce55267cfa6de8fa535989c3bcde873130ae62447ff7dc1298373964caf42 | C++ | 20,825 | 571 | //! \file us_style.cpp
#include "us_style.h"
#include "us_theme.h"
namespace
{
//! The palette group that matches the state a widget is painted in.
/*! Doing this explicitly rather than relying on the palette's current
group is what makes the "disabled" and "inactive" colors of the color
configu... |
b0f54b3ca895bd2eafc4bc87e210f1c1d8b2388f74c8355ec2cb1a4da8e2c1bd | C++ | 20,916 | 497 | //! \file us_model_select.cpp
#include "us_model_select.h"
#include "us_model_adpars.h"
#include "us_long_messagebox.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_sleep.h"
// Main constructor with model index, models list, additional parameters list
US_ModelSelect::US_ModelSelect(
int& ... |
bca59d6b6077368ec4f1a6e99eb6a54bbf2b3d9716f5590aa423a83d0dd10274 | C++ | 20,937 | 750 | // test_us_timer.cpp
#include <gtest/gtest.h>
#include <gmock/gmock.h>
#include "qt_test_base.h"
#include "us_timer.h"
#include <QTest>
#include <QThread>
#include <QEventLoop>
#include <QTimer>
using ::testing::_;
using ::testing::Return;
using ::testing::HasSubstr;
using ::testing::Not;
using ::qt_matchers::QStringC... |
0a6323bba336f5b6b597fa37bb66b657b5c31707d12a2eb330c1b1ce4a94f525 | C++ | 20,956 | 553 | //! \file us_adv_dmgamc.cpp
#include "us_adv_dmgamc.h"
#include "us_fematch.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "qwt_legend.h"
// constructor: advanced analysis control widget
US_AdvDmgaMc::US_AdvDmgaMc( US_Model* amodel,
QVector< US_Model >& aimodels,
QMa... |
b96a024378ddd3a274aadc64f412262d3fa0fe3133df215204216e1729e59b99 | C++ | 20,997 | 329 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement command
int t = 0; // time
static const int x_s... |
403bffdda906ff08253c2322c4fc73aec0e89b3d3d588ac66c3887725bf0abb0 | C++ | 21,030 | 544 | /** \file
*
* Unit tests for `KmerPresenceMatrix` and for the kmer presence iterators in
* `Haplotypes::Subchain`.
*/
#include "catch.hpp"
#include "../recombinator_haplotypes.hpp"
#include <random>
#include <sstream>
#include <string>
#include <vector>
namespace vg {
namespace unittest {
//-------------------... |
66be463844b5e38494e01908abbfc50451300a4107d187f332c84b3ba7a95db7 | C++ | 21,062 | 410 | // protein_psv.cpp -- whole-protein psv three ways, against measured values.
//
// Answers the question Mattia put: trust the tabulated amino-acid psv set, or the one derived
// from the atomic volume increments? The residue-level four-way table localises the differences
// but cannot say which is RIGHT; only a protein... |
b1f08a796fd238a397beba3000f657c358fa625b7cd135a7e19e8dcfcae69002 | C++ | 21,285 | 625 |
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <vector>
#include <string>
#include <set>
#include <map>
#include <utility>
#include <algorithm>
#include <numeric>
#include <cstdio>
#include <cstdlib>
#include <cassert>
#include <cmath>
#include "omp.h"
#include "format.hpp"
#inc... |
b72990b641467e4b8ffbdaeec08a6d8133db462cca5188fad084de36d8827400 | C++ | 21,314 | 659 | //! \file us_colorgradient.cpp
#include <QApplication>
#include "us_colorgradient.h"
#include "us_defines.h"
#include "us_license.h"
#include "us_license_t.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_util.h"
//const qreal lgndfrac=0.33333; // legend 1/3th of width (1 x 2)
const qreal lgndf... |
f2938b8aa78ade67db809f56e264253be7692a178cb44717634550eede1df2c4 | C++ | 21,346 | 802 | /******************************************************************************
SparkFunSX1509.cpp
SparkFun SX1509 I/O Expander Library Source File
Jim Lindblom @ SparkFun Electronics
Original Creation Date: September 21, 2015
https://github.com/sparkfun/SparkFun_SX1509_Arduino_Library
Here you'll find the Arduino cod... |
771f623d74c9fc1a6efb3186e3f399ec78ce4499427e99fecec8d7101d4370bf | C++ | 21,359 | 520 | #include "us_mpi_analysis.h"
#include "us_constants.h"
#include "us_math2.h"
#include "us_astfem_rsa.h"
#include "us_simparms.h"
#include "us_sleep.h"
void US_MPI_Analysis::pcsa_worker( void )
{
bool repeat_loop = true;
MPI_Job job;
MPI_Status status;
DbgLv(1) << "w:" << my_rank << ": pcsa_worker IN";
... |
8c24ea4ed01d82749bb1646966124ece3c43c9ddcddd7cb8e4947e61bbddf8c7 | C++ | 21,383 | 657 | #include <cstdint>
#include <numeric>
#include <sstream>
#include <string>
#include <unordered_set>
#include <cereal/archives/binary.hpp>
#include <cereal/types/string.hpp>
#include <cereal/types/vector.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/g... |
0a495977fbd595f60374928788e94c1441f863d061873b3642b8bc29d3b1c830 | C++ | 21,437 | 436 | #include "subgraph.hpp"
#include "../path.hpp"
#include "../crash.hpp"
namespace vg {
namespace algorithms {
void expand_subgraph_by_steps(const HandleGraph& source, MutableHandleGraph& subgraph, const uint64_t& steps, bool forward_only) {
std::vector<handle_t> curr_handles;
subgraph.for_each_handle([&](const... |
a7fdd30b6e6c731689176a7be8dad8505731355a37093c7e8cff54f5d90cdc77 | C++ | 21,481 | 677 | //! \file us_query_rmsd.cpp
#include <QApplication>
#include "us_query_rmsd.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_select_runs.h"
#include <QTemporaryDir>
//! \brief Main program. Loads the Model RMSD values from DB
int main( int argc,... |
92cabba5367f7933d181d236273c4556768844a04102fbe2367b91bf44b51b10 | C++ | 21,494 | 752 | //! \file us_predict2.cpp
#include "us_predict2.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include "us_model.h"
#include "us_buffer_gui.h"
#include "us_analyte_gui.h"
#include "us_constants.h"
#include "us_solution_gui.h"
#include "us_choice.h"
US_Predict2::US_Predict2() : US_Widgets()
{
model = SED... |
4e0e2126010be6814f3be6d1ccdd3aa4d19000ee156e2abf28087f84121e0931 | C++ | 21,524 | 703 | //! \file us_distrib_plot.cpp
#include "us_distrib_plot.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include <qwt_legend.h>
US_DistribPlot::US_DistribPlot( QVector< double >& divfracs,
QVector< double >& divsedcs, const double tconc )
: US_WidgetsDialo... |
a0d56dd64869975c29939ac389a72bd3f9e7c66c37680b68916db5b300a66f72 | C++ | 21,536 | 597 | /** \file rna_main.cpp
*
* Defines the "vg rna" subcommand.
*/
#include <unistd.h>
#include <getopt.h>
#include <chrono>
#include "subcommand.hpp"
#include "../transcriptome.hpp"
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include "../gbwt_helper.hpp"
#include "bdsg/packed_graph.hpp"
#include <gbwtgrap... |
8eace26596e64388d323fc662b7b68dedee3146697d92258766e2b446a90418d | C++ | 21,750 | 480 | #include "nested_flow_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
NestedFlowCaller::NestedFlowCaller(const PathPositionHandleGraph& graph,
SupportBasedSnarlCaller... |
18fb189578e34ede5193b8b5f0016e93a21b23a2486f5b684e7b8308184c72cc | C++ | 21,820 | 682 | //! \file us_xpnhost.cpp
#include "us_xpnhost.h"
#include "us_xpn_data.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_passwd.h"
#include "us_help.h"
#include "us_crypto.h"
#include "us_db2.h"
#define def_desc QString("place-holder")
#define def_host QString("192.168.1.1")
#define def_port QStrin... |
438bd649f6128cd3671077975ff759521a48fc717d84a3dd4ec3dc09084ac85b | C++ | 21,824 | 862 | #include "MaterialGrid.hpp"
#include <sstream>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <limits>
#include <algorithm>
#include <queue>
#include <tuple>
#include <utility>
#include <cstdio>
#include <cmath>
#include "Random.hpp"
const GReal MaterialGrid::PI = 3.141592;
MaterialGrid::Materi... |
51aebd2e7a282916724d367d31301e28941a7ce8a06959e99d2a2afe31f2ca1a | C++ | 22,012 | 536 | #include "subcommand.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../utility.hpp"
#include "../mapper.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include "../alignment.hpp"
#include "../annotation.hpp"
#include "../gff_reader.hpp"
#include "../region_expander.hpp"
#include "../algorithms/ali... |
f1fe9b89d8889ee10437bbf486229b0f4e112639ec509f965cacf922562bbc1a | C++ | 22,202 | 639 | /// \file mapper.cpp
///
/// unit tests for the mapper
#include <iostream>
#include "vg/io/json2pb.h"
#include "../io/json2graph.hpp"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
#include "../mapper.hpp"
#include "xg.hpp"
#include "../build_index.hpp"
#include "catch.hpp"
#include "../algorithms/alignment_path... |
96c88bbcc851361461288c12af077c7f3def0a161e35d1f4f2a149044bf6d685 | C++ | 22,224 | 544 |
/*
compile with:
g++ -std=c++11 -lz -o x x.cpp
*/
#include <cstring> // memcpy on Linux
#include <algorithm> // count on Linux
#include <stdexcept> // runtime_error on Linux
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <string>
#include <glob.h>
#include <stdlib.h>
#include ... |
218aec2615bf92e0d07d06083c60107e1b82e79f6a36bad0c940e53ee20d7939 | C++ | 22,264 | 742 | //! file us_equiltime.cpp
#include "us_equiltime.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_settings.h"
#include "us_constants.h"
#include "us_math2.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_model_gui.h"
//! \brief Main program for US_Equilspeed. Loads translators and... |
66579bae9a6f4be8dfe8a3a07400dfa639570d9e4180deb65e7c33780f549b51 | C++ | 22,295 | 645 | #include <fstream>
#include <numeric> // std::iota
#include <sstream>
#include <string>
#include <string_view>
#include <vector>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#include <graphtyper/graph/graph_serialization.hp... |
f957a06c30f8bb4c3e256af1e3a1b8aa1552132cf9689972bb08dcd696a26aec | C++ | 22,424 | 652 | /*
Copyright (c) 2006-2010, The Scripps Research Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless requir... |
923e3ee548dc3996f14cdd1735b10b6b01f6a8e86e82eb548dc95d9fa39bb754 | C++ | 22,458 | 681 | #include <cassert>
#include <cstdint> // uint32_t
#include <cstdlib> // abs
#include <iomanip>
#include <ios>
#include <unordered_map>
#include <utility>
#include <cereal/archives/binary.hpp>
#include <cereal/types/map.hpp>
#include <cereal/types/set.hpp>
#include <cereal/types/string.hpp>
#include <cereal/types/unord... |
1bf8ed477edd4682e32f3ef867f31fd1fd7141d943daf9c3104be60127acf97e | C++ | 22,518 | 695 | #include <algorithm>
#include <cassert>
#include <cstdlib>
#include <iostream>
#include <iterator>
#include <set>
#include <time.h>
#include <utility>
#include <parallel_hashmap/phmap.h>
#include <paw/station.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#... |
f0fec6fc1e499f88f4d86896e961eb37fafd90e298914b6ea377b2096528e692 | C++ | 22,575 | 542 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
618fc6ae0c2b7c745ce600c00eda262e7e140dd609fe77ede92bfae6d51bc31f | C++ | 22,784 | 450 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
be52424de1b1ab16cce05e536fc6645550387d015f501896b7842fa12f5c55e9 | C++ | 22,869 | 715 | //! \file us_report_general_gui.cpp
#include "us_report_general_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_images.h"
US_ReportGenGui::US_ReportGenGui( QString reportMask ) : US_Widgets()
{
this->reportMask = repor... |
f0e4824eb009f4cc99051867d64882f018186f22a507966d8b8c92546cbed56e | C++ | 22,898 | 496 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ee08bb03a3aabf94605837a3473f8c985b5f40d9eccf9b148ae7b0dc740b0aac | C++ | 23,005 | 708 | //! \file us_predict1.cpp
#include "us_predict1.h"
#include "us_constants.h"
#include "us_gui_settings.h"
#include "us_buffer_gui.h"
#include "us_choice.h"
#include "us_solution_gui.h"
#include "us_math2.h"
#if QT_VERSION > 0x050000
#include "qwt_point_data.h"
#else
#define setSamples(a,b,c) setData(a,b,c)
#endif
#inc... |
f0669d64bd3a773355088c6b740b07715e4adf12f0b4a35bc9067941c336af94 | C++ | 23,083 | 777 | //! \file us_database.cpp
#include "us_database.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_passwd.h"
#include "us_help.h"
#include "us_crypto.h"
#include "us_db2.h"
#include "us_local_server.h"
#ifndef DbgLv
#define DbgLv(a) if(dbg_level>=a)qDebug() //!< debug-level-conditioned qDebug()
#end... |
a1a8627cc1441931938006c0f45bc40ad7908e277a1507cce2f339b48f19ba30 | C++ | 23,168 | 529 | /**
* \file extract_connecting_graph.cpp
*
* Implementation for the extract_connecting_graph algorithm.
*/
#include "extract_connecting_graph.hpp"
#include <structures/updateable_priority_queue.hpp>
#include "../crash.hpp"
//#define debug_vg_algorithms
namespace vg {
namespace algorithms {
using namespace stru... |
3f8471a6f09dde8ecf49d991b6ac814a824fc709248e7bd7b5a25262b6841f48 | C++ | 23,209 | 582 | #include "catch.hpp"
#include "../handle.hpp"
#include "../vg.hpp"
#include "../io/json2graph.hpp"
#include "xg.hpp"
#include "bdsg/packed_graph.hpp"
#include "bdsg/hash_graph.hpp"
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("copy_handle_graph converter wor... |
88d74a6ca5699d72e481f928d6f8abaeb68cec063eaf59aa77fd1484b5d6b2c4 | C++ | 23,304 | 714 | //! \file us_experiment_ra.cpp
#include "us_settings.h"
#include "us_db2.h"
#include "us_passwd.h"
#include "us_investigator.h"
#include "us_util.h"
#include "us_experiment_ra.h"
US_ExperimentRa::US_ExperimentRa( void )
{
// Experiment types
experimentTypes.clear();
experimentTypes << "Velocity"
... |
e5d86a531eea078f5c1bba09ac67cb918a4eac495372d00328111e7214358b32 | C++ | 23,401 | 779 | //! \file us_experiment_gui_ra.cpp
#include "us_experiment_gui_ra.h"
#include "us_passwd.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_project_gui.h"
#include "us_rotor_gui.h"
US_ExperimentGuiRa::US_ExperimentGuiRa(
bool signal_wanted,
... |
f54806d6c30792ea90eac575397b977dab4bee6f6a3e14415af5eba7345b078b | C++ | 23,580 | 545 | #include "primer_filter.hpp"
#include <unordered_set>
#include "surjector.hpp"
#include "hts_alignment_emitter.hpp"
namespace vg {
using namespace std;
//#define DEBUG_PRIMER_FILTER
// Constructor
PrimerFinder::PrimerFinder(const unique_ptr<handlegraph::PathPositionHandleGraph>& graph_param,
const SnarlDistance... |
7063fa66c005644df3a030b614852362a5c2db19de42b57bc5801d3f0e2c5e5b | C++ | 23,636 | 660 | #include "stream_index.hpp"
#include <iostream>
#include <queue>
#include "algorithms/sorted_id_ranges.hpp"
#include <google/protobuf/io/zero_copy_stream_impl.h>
#include <google/protobuf/io/gzip_stream.h>
namespace vg {
using namespace std;
BitString::BitString(uint64_t bits, size_t length) : bits(bits), bit_leng... |
80bd8ce5171e4b9fceb86104f78259012854dcccaa2288a017db83875bb8944a | C++ | 23,649 | 606 | /** \file
*
* Unit tests for the PhaseUnfolder, which replaces pruned regions of the
* graph with paths supported by XG paths or GBWT threads.
*/
#include <iostream>
#include <map>
#include <omp.h>
#include <gbwt/dynamic_gbwt.h>
#include "../phase_unfolder.hpp"
#include "../io/json2graph.hpp"
#include <bdsg/has... |
9f3458440ec281d6f72a87b600e599f960cb21524893825216499309c49d8944 | C++ | 23,795 | 657 | #include "path_index.hpp"
namespace vg {
PathIndex::PathIndex(const Path& path) {
// Just trace the path, which we assume has mapping lengths filled in.
// What base are we at in the path?
size_t path_base = 0;
// What was the last rank? Ranks must always go up.
int64_t last_rank = -1;
... |
b828737a6ed56880a6e2457dca21e9d90950341d7132a2b3b826f6086a977ef5 | C++ | 23,959 | 809 | //! \file us_investigator.cpp
#include "us_investigator.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_db2.h"
#include "us_crypto.h"
#include "us_passwd.h"
/*! Construct a new US_Investigator interface.
*/
US_Investigator::US_Investigator( bool signal, int inv )
: US_WidgetsDialog( nullptr,... |
06f4cc8fcb1bf67a3dd7a80336bd4edc239c2430707e3641cd63d154f436a0ee | C++ | 24,121 | 831 | //! \file us_resplot_pc.cpp
#include "us_resplot_pc.h"
#include "us_pcsa.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_constants.h"
#include <qwt_legend.h>
// constructor: residuals plot widget
US_ResidPlotPc::US_ResidPlotPc( QWidget* parent )
... |
14e7f9b5f876db46031d270e153ec47831144cdf358faa34c879ca0489628e2a | C++ | 24,219 | 589 | /** \file filter_main.cpp
*
* Defines the "vg filter" subcommand, which filters alignments.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../readfilter.hpp"
#include <vg/io/vpkg.hpp>
#i... |
6818ec7e9335158d16f9bb3acaa5875568b7113bfe87e369e7717a6a1e0b925c | C++ | 24,614 | 592 | /*# Copyright (C) 2019 Andrea Vázquez Varela
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distri... |
cda770b9cc28da8a0a912a6f0f6805a5716eebe8cdb6d6ae6ba330c891ed76c7 | C++ | 24,615 | 671 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
b4d345c4fcd8dd31b9d84fb925efa6bee39059e34c8b3a2d8c58de12fb2e3f70 | C++ | 24,726 | 819 | //! \file us_experiment_gui.cpp
#include "us_experiment_gui.h"
#include "us_passwd.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_project_gui.h"
#include "us_rotor_gui.h"
#include "us_convertio.h"
US_ExperimentGui::US_ExperimentGui(
bool s... |
5f4f9c1cc0618bff200d4a6468708494ef5fcabeb2c92c7bbd65568fd21f748f | C++ | 24,752 | 639 | //! \file us_mlplot.cpp
#include "us_mlplot.h"
#include "us_pcsa.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_zsolute.h"
#include "us_colorgradIO.h"
#include <qwt_legend.h>
#include <qwt_scale_widget.h>
#include <qwt_color_map.h>
#include <qwt_sc... |
6cda9014899177a7423b281a56e0ff58eafe21c584d6fe6dcdf4c530c45cdf06 | C++ | 24,875 | 671 | /**
* \file statistics.cpp
*
* Contains implementations of statistical functions
*
*/
#include "statistics.hpp"
namespace vg {
double median(std::vector<int> &v) {
size_t n = v.size() / 2;
std::nth_element(v.begin(), v.begin()+n, v.end());
int vn = v[n];
if (v.size()%2 == 1) {
return vn... |
73993f942a5efb2808d39815d2295e5dc40c73eff531135f374ed1b26647b1b1 | C++ | 24,896 | 851 | //! \file us_resplot_2d.cpp
#include "us_resplot_2d.h"
#include "us_2dsa.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_constants.h"
#include <qwt_legend.h>
// constructor: residuals plot widget
US_ResidPlot2D::US_ResidPlot2D( QWidget* parent )
... |
045b5b79d3ae98f007d939491cbf439c61f61eedd362fea41863714bcfd0b8c1 | C++ | 25,013 | 655 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
fddcf983872901bf96ef2aad71af9173d72e53a5ca7496d3b3729883a3c5b10d | C++ | 25,055 | 713 | #include "gaf_sorter.hpp"
#include <chrono>
#include <cmath>
#include <deque>
#include <fstream>
#include <queue>
#include <thread>
#include <charconv>
// Needed for the temporary file creation.
#include "utility.hpp"
// For reading and writing compressed temporary files.
#include "zstdutil.hpp"
// For reading comp... |
657ad17a9b19b49fac4ba01b6f98759c92f5a8b836aeb08b9bd6e1b7f7bb83f1 | C++ | 25,304 | 830 | //! \file us_run_details2.cpp
#include "us_run_details2.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_math2.h"
#include "us_constants.h"
#include "us_util.h"
#include "us_gui_util.h"
#include <qwt_legend.h>
#include <qwt_plot_layout.h>
#include <qwt_plot_curve.h>
#include <qwt_scale_widget.h>
... |
2df5b36eda2c525d2a2f57af5d86df25d8fb658b8af9d0f23a79dff9dd48218f | C++ | 25,369 | 784 | #define ALT_SH
#define ALT_SPHBES
#include "pm_worker.h"
bool PM_WORKER::compute_I( set < pm_point > & model, vector < double > & I_result )
{
if ( !model.size() )
{
error_msg = "empty model";
return false;
}
if ( use_CYJ )
{
return compute_CYJ_I( model, I_result );
} else {
... |
613016db03ed85a848b8cda2ef1c724344e9b87b509675e9aebbf467ebb55cb3 | C++ | 25,546 | 747 | //! \file us_manage_data.cpp
#include <QApplication>
#include "us_manage_data.h"
#include "us_data_model.h"
#include "us_data_tree.h"
#include "us_data_process.h"
#include "us_select_item.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_matrix.h"
#include "us_constants.h"
#include "us_license_t.h... |
c64961efa1f4a0833893dadc78b973d6161dc16f9cea1c78bd907ebceb1f4375 | C++ | 25,581 | 442 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
f86d615f765067356f6854ed4bfc376bbabc3be6410221933220853364f8f458 | C++ | 25,591 | 817 | //! \file us_buoyancy.cpp
#include <QApplication>
#include <QDomDocument>
#include "us_fds_filemanager.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_util.h"
#include "us_passwd.h"
#include "us_db2.h"
#ifndef DbgLv
#def... |
bf27a7ff860ef02e8f2ea5d69f92a7a8bdbf98b58419ff4787692f8c82412082 | C++ | 25,993 | 630 | #include "alignment_scorer.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <cstdlib>
#include <iostream>
#include <limits>
#include "alignment.hpp"
#include "crash.hpp"
#include "gssw.h"
//#define debug
namespace vg {
using std::function;
using std::max;
using std::min;
using std::string;
us... |
c54e9ae61087f636771e677e743fccd52e737f9f2fcaf55938b5adeabfd0f4f8 | C++ | 26,154 | 606 | /// \file multipath_mapper.cpp
///
/// unit tests for the multipath mapper
#include <iostream>
#include "vg/io/json2pb.h"
#include "../io/json2graph.hpp"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
#include "../multipath_mapper.hpp"
#include "../build_index.hpp"
#include "xg.hpp"
#include "vg.hpp"
#include ... |
d2531fd0576393f892130242dd0ead83b6bc5a627eae2fb13a292d78b1de6307 | C++ | 26,168 | 569 | #include "flow_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
FlowCaller::FlowCaller(const PathPositionHandleGraph& graph,
SupportBasedSnarlCaller& snarl_caller,
... |
13464fea31153b09c91d93afe7170231b76eaac83634f5d7a8b2b57b7b564be9 | C++ | 26,240 | 591 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
37bc4de86ade6dcbdb75a1188bbfd21715353fd8dd25e2809d139ec2ed3f1315 | C++ | 26,304 | 956 | #include <qmetaobject.h>
#include <qframe.h>
#include <qlabel.h>
#include <qpushbutton.h>
#include <qlayout.h>
#include <qtooltip.h>
#include <qwhatsthis.h>
#include <qaction.h>
#include <qmenubar.h>
#if QT_VERSION < 0x040000
#include <qpopupmenu.h>
#endif
#include <qtoolbar.h>
#include <qimage.h>
#... |
88703cb8346eaf120335af6757968e989da05ab86197196168173d4125a68519 | C++ | 26,357 | 741 | #include <algorithm>
#include <cassert>
#include <iostream>
#include <sstream>
#include <string>
#include <utility>
#include <vector>
#include <paw/station.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#include <grapht... |
72dcf00ac19712359ca7035943a2c42a97e03b2e713d21c915be4d74d3bd802c | C++ | 26,455 | 642 | // index.cpp: define the "vg index" subcommand, which makes XG, GCSA2, and distance indexes
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <random>
#include <string>
#include <vector>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "xg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg... |
ee7a2e35bc6f865dc61047dcb673d76e6c33f53dd08a0edd4c4c29a7fb18d6d0 | C++ | 26,544 | 607 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
8b10fdc07cf3d710609d8d90cb5fc740358c5ef4005db747a9134df214ca9517 | C++ | 26,576 | 683 | #include "genotypekit.hpp"
#include "cactus.hpp"
#include "traversal_finder.hpp"
//#define debug
namespace vg {
using namespace std;
SnarlTraversal get_traversal_of_snarl(VG& graph, const Snarl* snarl, const SnarlManager& manager, const Path& path) {
// We'll fill this in
SnarlTraversal to_return;
aut... |
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