diff --git a/.gitignore b/.gitignore
index b6ae1c93..5570830b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ docs/sphinx_build
docs/sphinx_build_man
docs/_build
Testing/
+.idea/
\ No newline at end of file
diff --git a/.gitmodules b/.gitmodules
index 80286b42..131bf282 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -45,7 +45,7 @@
url = https://github.com/jeizenga/structures.git
[submodule "deps/libbf"]
path = deps/libbf
- url = https://github.com/mavam/libbf.git
+ url = https://github.com/subwaystation/libbf.git
[submodule "deps/cpp-httplib"]
path = deps/cpp-httplib
url = https://github.com/yhirose/cpp-httplib.git
diff --git a/deps/libbf b/deps/libbf
index 5478275d..6ac3c11c 160000
--- a/deps/libbf
+++ b/deps/libbf
@@ -1 +1 @@
-Subproject commit 5478275d8a4e9a5cc163b44c34517c515bd898ec
+Subproject commit 6ac3c11c73b629130cc63618669c1be53d428c80
diff --git a/deps/libhandlegraph b/deps/libhandlegraph
index 900f3a8f..772d1637 160000
--- a/deps/libhandlegraph
+++ b/deps/libhandlegraph
@@ -1 +1 @@
-Subproject commit 900f3a8f6bf8615e8446bf63f70077d5cff5f7fa
+Subproject commit 772d16374e6f46791378c3d9ba87445216b76a08
diff --git a/deps/pybind11 b/deps/pybind11
index 98f1bbb8..0e43fcc7 160000
--- a/deps/pybind11
+++ b/deps/pybind11
@@ -1 +1 @@
-Subproject commit 98f1bbb8004f654ba9e26717bdf5912fb899b05a
+Subproject commit 0e43fcc75e6b7429e3511dfb44343ec05a0ab843
diff --git a/scripts/heaps_fit.R b/scripts/heaps_fit.R
index 88c69dfe..6e2338ac 100644
--- a/scripts/heaps_fit.R
+++ b/scripts/heaps_fit.R
@@ -31,6 +31,6 @@ n <- max(x$nth.genome)
print(z * (f(n) - f(n-1)))
print(z * (f(2) - f(1)))
#print(f(n) - f(n-1))
-
-ggplot(x, aes(x=nth.genome, y=base.pairs/1e9)) + geom_point(alpha=I(1/10)) + stat_function(fun=function(x) (fit$par[1] * x^fit$par[2] + fit$par[3]) * m) + scale_y_continuous("observed pangenome size (Gbp)") + scale_x_continuous("Nth included genome (200 permutations)")
+pdf(NULL)
+ggplot(x, aes(x=nth.genome, y=base.pairs/1e9)) + geom_point(alpha=I(1/10)) + stat_function(fun=function(x) (fit$par[1] * x^fit$par[2] + fit$par[3]) * m) + scale_y_continuous("observed pangenome size (Gbp)") + scale_x_continuous(paste("Nth included genome (", max(x$permutation)+1 ," permutations) with gamma=", round(fit$par[2], digits=3), sep = "")) + expand_limits(x = 0, y = 0)
ggsave(args[2], height=5, width=9)
diff --git a/src/algorithms/progress.hpp b/src/algorithms/progress.hpp
index 4137cf96..e0eb271f 100644
--- a/src/algorithms/progress.hpp
+++ b/src/algorithms/progress.hpp
@@ -15,86 +15,81 @@ namespace algorithms {
namespace progress_meter {
-class ProgressMeter {
-public:
- std::string banner;
- std::atomic<uint64_t> total;
- std::atomic<uint64_t> completed;
- std::chrono::time_point<std::chrono::steady_clock> start_time;
- std::thread logger;
- ProgressMeter(uint64_t _total, const std::string& _banner)
- : total(_total), banner(_banner) {
- start_time = std::chrono::steady_clock::now();
- completed = 0;
-
- logger = std::thread(
- [&]() {
- bool has_ever_printed = false;
-
- while (completed < total) {
- if (completed > 0) {
+ class ProgressMeter {
+ public:
+ std::string banner;
+ std::atomic<uint64_t> total;
+ std::atomic<uint64_t> completed;
+ std::chrono::time_point<std::chrono::steady_clock> start_time;
+ std::thread logger;
+ ProgressMeter(uint64_t _total, const std::string& _banner)
+ : total(_total), banner(_banner) {
+ start_time = std::chrono::steady_clock::now();
+ completed = 0;
+ logger = std::thread(
+ [&](void) {
do_print();
- has_ever_printed = true;
- }
- if (has_ever_printed && completed < total) {
- std::this_thread::sleep_for(std::chrono::milliseconds(250));
- } else {
- std::this_thread::sleep_for(std::chrono::nanoseconds(100));
- }
- }
- });
+ auto last = 0;
+ while (completed < total) {
+ auto curr = completed - last;
+ if (curr > 0) {
+ do_print();
+ last = completed;
+ }
+ std::this_thread::sleep_for(std::chrono::milliseconds(500));
+ }
+ });
+ };
+ void do_print(void) {
+ auto curr = std::chrono::steady_clock::now();
+ std::chrono::duration<double> elapsed_seconds = curr-start_time;
+ double rate = completed / elapsed_seconds.count();
+ double seconds_to_completion = (completed > 0 ? (total - completed) / rate : 0);
+ std::cerr << "\r" << banner << " "
+ << std::defaultfloat
+ << std::setfill(' ')
+ << std::setw(5)
+ << std::fixed
+ << std::setprecision(2)
+ << 100.0 * ((double)completed / (double)total) << "%"
+ << " @ "
+ << std::setw(4) << std::scientific << rate << " bp/s "
+ << "elapsed: " << print_time(elapsed_seconds.count()) << " "
+ << "remain: " << print_time(seconds_to_completion);
+ }
+ void finish(void) {
+ completed.store(total);
+ logger.join();
+ do_print();
+ std::cerr << std::endl;
+ }
+ std::string print_time(const double& _seconds) {
+ int days = 0, hours = 0, minutes = 0, seconds = 0;
+ distribute_seconds(days, hours, minutes, seconds, _seconds);
+ std::stringstream buffer;
+ buffer << std::setfill('0') << std::setw(2) << days << ":"
+ << std::setfill('0') << std::setw(2) << hours << ":"
+ << std::setfill('0') << std::setw(2) << minutes << ":"
+ << std::setfill('0') << std::setw(2) << seconds;
+ return buffer.str();
+ }
+ void distribute_seconds(int& days, int& hours, int& minutes, int& seconds, const double& input_seconds) {
+ const int cseconds_in_day = 86400;
+ const int cseconds_in_hour = 3600;
+ const int cseconds_in_minute = 60;
+ const int cseconds = 1;
+ days = std::floor(input_seconds / cseconds_in_day);
+ hours = std::floor(((int)input_seconds % cseconds_in_day) / cseconds_in_hour);
+ minutes = std::floor((((int)input_seconds % cseconds_in_day) % cseconds_in_hour) / cseconds_in_minute);
+ seconds = ((((int)input_seconds % cseconds_in_day) % cseconds_in_hour) % cseconds_in_minute) / cseconds; // + (input_seconds - std::floor(input_seconds));
+ //std::cerr << input_seconds << " seconds is " << days << " days, " << hours << " hours, " << minutes << " minutes, and " << seconds << " seconds." << std::endl;
+ }
+ void increment(const uint64_t& incr) {
+ completed += incr;
+ }
};
- void do_print() {
- auto curr = std::chrono::steady_clock::now();
- std::chrono::duration<double> elapsed_seconds = curr-start_time;
- double rate = completed / elapsed_seconds.count();
- double seconds_to_completion = (total - completed) / rate;
- std::cerr << "\r" << banner << " "
- << std::defaultfloat
- << std::setfill(' ')
- << std::setw(5)
- << std::fixed
- << std::setprecision(2)
- << 100.0 * ((double)completed / (double)total) << "%"
- << " @ "
- << std::setw(4) << std::scientific << rate << "/s "
- << "elapsed: " << print_time(elapsed_seconds.count()) << " "
- << "remain: " << print_time(seconds_to_completion);
- }
- void finish() {
- completed.store(total);
- logger.join();
- do_print();
- std::cerr << std::endl;
- }
- std::string print_time(const double& _seconds) {
- int days = 0, hours = 0, minutes = 0, seconds = 0;
- distribute_seconds(days, hours, minutes, seconds, _seconds);
- std::stringstream buffer;
- buffer << std::setfill('0') << std::setw(2) << days << ":"
- << std::setfill('0') << std::setw(2) << hours << ":"
- << std::setfill('0') << std::setw(2) << minutes << ":"
- << std::setfill('0') << std::setw(2) << seconds;
- return buffer.str();
- }
- void distribute_seconds(int& days, int& hours, int& minutes, int& seconds, const double& input_seconds) {
- const int cseconds_in_day = 86400;
- const int cseconds_in_hour = 3600;
- const int cseconds_in_minute = 60;
- const int cseconds = 1;
- days = std::floor(input_seconds / cseconds_in_day);
- hours = std::floor(((int)input_seconds % cseconds_in_day) / cseconds_in_hour);
- minutes = std::floor((((int)input_seconds % cseconds_in_day) % cseconds_in_hour) / cseconds_in_minute);
- seconds = ((((int)input_seconds % cseconds_in_day) % cseconds_in_hour) % cseconds_in_minute) / cseconds; // + (input_seconds - std::floor(input_seconds));
- //std::cerr << input_seconds << " seconds is " << days << " days, " << hours << " hours, " << minutes << " minutes, and " << seconds << " seconds." << std::endl;
- }
- void increment(const uint64_t& incr) {
- completed += incr;
- }
-};
}
}
-
}
diff --git a/src/odgi.cpp b/src/odgi.cpp
index b97f31da..0adc8c86 100644
--- a/src/odgi.cpp
+++ b/src/odgi.cpp
@@ -781,7 +781,7 @@ void graph_t::reassign_node_ids(const std::function<nid_t(const nid_t&)>& get_ne
/// Reorder the graph's internal structure to match that given.
/// Optionally compact the id space of the graph to match the ordering, from 1->|ordering|.
-void graph_t::apply_ordering(const std::vector<handle_t>& order_in, bool compact_ids) {
+bool graph_t::apply_ordering(const std::vector<handle_t>& order_in, bool compact_ids) {
// get mapping from old to new id
// if we're given an empty order, just compact the ids based on our ordering
const std::vector<handle_t>* order;
@@ -894,6 +894,8 @@ void graph_t::apply_ordering(const std::vector<handle_t>& order_in, bool compact
}
node_v = new_node_v;
deleted_nodes.clear();
+
+ return true;
}
void graph_t::apply_path_ordering(const std::vector<path_handle_t>& order) {
diff --git a/src/odgi.hpp b/src/odgi.hpp
index 7f2d5eb1..adfa7f14 100644
--- a/src/odgi.hpp
+++ b/src/odgi.hpp
@@ -305,7 +305,7 @@ class graph_t : public MutablePathDeletableHandleGraph, public SerializableHandl
/// Reorder the graph's internal structure to match that given.
/// Optionally compact the id space of the graph to match the ordering, from 1->|ordering|.
- void apply_ordering(const std::vector<handle_t>& order, bool compact_ids = false);
+ bool apply_ordering(const std::vector<handle_t>& order, bool compact_ids = false);
/// Organize the graph for better performance and memory use
void optimize(bool allow_id_reassignment = true);
diff --git a/src/subcommand/heaps_main.cpp b/src/subcommand/heaps_main.cpp
index 890dccef..0a340df1 100644
--- a/src/subcommand/heaps_main.cpp
+++ b/src/subcommand/heaps_main.cpp
@@ -128,6 +128,11 @@ int main_heaps(int argc, char **argv) {
auto vals = split(path_name, '#');
path_groups_map[vals.front()].push_back(p);
});
+ } else {
+ // no groups
+ graph.for_each_path_handle([&](const path_handle_t& p) {
+ path_groups_map[graph.get_path_name(p)].push_back(p);
+ });
}
path_groups.reserve(path_groups_map.size());
for (auto& g : path_groups_map) {
diff --git a/src/subcommand/overlap_main.cpp b/src/subcommand/overlap_main.cpp
index dc6c0a79..176b51da 100644
--- a/src/subcommand/overlap_main.cpp
+++ b/src/subcommand/overlap_main.cpp
@@ -125,39 +125,6 @@ namespace odgi {
}
}
- auto get_graph_pos = [](const odgi::graph_t &graph,
- const path_pos_t &pos) {
- auto path_end = graph.path_end(pos.path);
- uint64_t walked = 0;
- for (step_handle_t s = graph.path_begin(pos.path);
- s != path_end; s = graph.get_next_step(s)) {
- handle_t h = graph.get_handle_of_step(s);
- uint64_t node_length = graph.get_length(h);
- if (walked + node_length > pos.offset) {
- return make_pos_t(graph.get_id(h), graph.get_is_reverse(h), pos.offset - walked);
- }
- walked += node_length;
- }
-
-#pragma omp critical (cout)
- std::cerr << "[odgi::overlap] warning: position " << graph.get_path_name(pos.path) << ":" << pos.offset
- << " outside of path" << std::endl;
- return make_pos_t(0, false, 0);
- };
-
- auto get_offset_in_path = [](const odgi::graph_t &graph,
- const path_handle_t &path, const step_handle_t &target) {
- auto path_end = graph.path_end(path);
- uint64_t walked = 0;
- step_handle_t s = graph.path_begin(path);
- for (; s != target; s = graph.get_next_step(s)) {
- handle_t h = graph.get_handle_of_step(s);
- walked += graph.get_length(h);
- }
- assert(s != path_end);
- return walked;
- };
-
if (!path_ranges.empty()) {
std::cout << "#path\tstart\tend\tpath.touched" << std::endl;
diff --git a/src/subcommand/version_main.cpp b/src/subcommand/version_main.cpp
index a3e95c85..be3b1d63 100644
--- a/src/subcommand/version_main.cpp
+++ b/src/subcommand/version_main.cpp
@@ -1,6 +1,7 @@
#include "subcommand.hpp"
#include "args.hxx"
#include "../version.hpp"
+#include <cstdint>
namespace odgi {