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Speed up XG construction when IDs don't start at 1 #3

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merged 4 commits into from
Jun 20, 2019
Merged

Speed up XG construction when IDs don't start at 1 #3

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4450fac
point to mac compilable ips4o and mmmultimap
jeizenga Jun 19, 2019
dc03bb0
turn off verbose debug
jeizenga Jun 19, 2019
1ce617b
switch handlegraph includes from system to local
jeizenga Jun 19, 2019
0a4c45f
allocate the right amount of disk space in gfa constructor
jeizenga Jun 19, 2019
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7 changes: 4 additions & 3 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdiv
# mmmultimap (memory mapped multimap)
ExternalProject_Add(mmmultimap
GIT_REPOSITORY "https://github.com/ekg/mmmultimap.git"
GIT_TAG "8a76cec0b819de6e2b855f4edc29993f75b1b26b"
GIT_TAG "b92a5c8826141d61413546278719724e0f612c39"
BUILD_COMMAND ""
UPDATE_COMMAND ""
INSTALL_COMMAND "")
Expand Down Expand Up @@ -109,8 +109,8 @@ set(gfakluge_tinyFA_INCLUDE "${INSTALL_DIR}/src/gfakluge/src/tinyFA")

# In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
ExternalProject_Add(ips4o
GIT_REPOSITORY "https://github.com/SaschaWitt/ips4o.git"
GIT_TAG "bff3ccf0bf349497f2bb10f825d160b792236367"
GIT_REPOSITORY "https://github.com/vgteam/ips4o.git"
GIT_TAG "22069381cc1bf2df07ee1ff47f6b6073fcfb4508"
INSTALL_COMMAND ""
BUILD_COMMAND ""
CONFIGURE_COMMAND "")
Expand All @@ -121,6 +121,7 @@ set(CMAKE_BUILD_TYPE Release)

add_library(xg_objs OBJECT src/xg.cpp)

add_dependencies(xg_objs handlegraph)
add_dependencies(xg_objs sdsl-lite)
add_dependencies(xg_objs mmmultimap)
add_dependencies(xg_objs tayweeargs)
Expand Down
34 changes: 17 additions & 17 deletions src/xg.cpp
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Expand Up @@ -11,7 +11,7 @@

#include "gfakluge.hpp"

#define VERBOSE_DEBUG
//#define VERBOSE_DEBUG
//#define debug_algorithms
//#define debug_component_index

Expand Down Expand Up @@ -383,31 +383,31 @@ void XG::from_gfa(const std::string& gfa_filename, bool validate, std::string ba
// set up our enumerators
auto for_each_sequence = [&](const std::function<void(const std::string& seq, const nid_t& node_id)>& lambda) {
gfa.for_each_sequence_line_in_file(filename, [&](gfak::sequence_elem s) {
nid_t node_id = std::stol(s.name);
lambda(s.sequence, node_id);
});
nid_t node_id = std::stol(s.name);
lambda(s.sequence, node_id);
});
};
auto for_each_edge = [&](const std::function<void(const nid_t& from_id, const bool& from_rev,
const nid_t& to_id, const bool& to_rev)>& lambda) {
gfa.for_each_edge_line_in_file(filename, [&](gfak::edge_elem e) {
if (e.source_name.empty()) return;
nid_t from_id = std::stol(e.source_name);
bool from_rev = !e.source_orientation_forward;
nid_t to_id = std::stol(e.sink_name);
bool to_rev = !e.sink_orientation_forward;
lambda(from_id, from_rev, to_id, to_rev);
});
if (e.source_name.empty()) return;
nid_t from_id = std::stol(e.source_name);
bool from_rev = !e.source_orientation_forward;
nid_t to_id = std::stol(e.sink_name);
bool to_rev = !e.sink_orientation_forward;
lambda(from_id, from_rev, to_id, to_rev);
});
};
auto for_each_path_element = [&](const std::function<void(const std::string& path_name,
const nid_t& node_id, const bool& is_rev,
const std::string& cigar)>& lambda) {
gfa.for_each_path_element_in_file(filename, [&](const std::string& path_name_raw, const std::string& node_id_str,
bool is_rev, const std::string& cigar) {
nid_t node_id = std::stol(node_id_str);
std::string path_name = path_name_raw;
path_name.erase(std::remove_if(path_name.begin(), path_name.end(), [](char c) { return std::isspace(c); }), path_name.end());
lambda(path_name, node_id, is_rev, cigar);
});
nid_t node_id = std::stol(node_id_str);
std::string path_name = path_name_raw;
path_name.erase(std::remove_if(path_name.begin(), path_name.end(), [](char c) { return std::isspace(c); }), path_name.end());
lambda(path_name, node_id, is_rev, cigar);
});
};
from_enumerators(for_each_sequence, for_each_edge, for_each_path_element, validate, basename);
}
Expand Down Expand Up @@ -587,7 +587,7 @@ void XG::from_enumerators(const std::function<void(const std::function<void(cons
edge_from_to_mm.append(as_integer(from_handle), as_integer(to_handle));
edge_to_from_mm.append(as_integer(to_handle), as_integer(from_handle));
});
handle_t max_handle = number_bool_packing::pack(max_id, true);
handle_t max_handle = number_bool_packing::pack(r_iv.size(), true);
edge_from_to_mm.index(as_integer(max_handle));
edge_to_from_mm.index(as_integer(max_handle));

Expand Down
16 changes: 5 additions & 11 deletions src/xg.hpp
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Expand Up @@ -22,17 +22,11 @@
#include "sdsl/csa_wt.hpp"
#include "sdsl/suffix_arrays.hpp"

#include <handlegraph/types.hpp>
#include <handlegraph/iteratee.hpp>
#include <handlegraph/util.hpp>
#include <handlegraph/handle_graph.hpp>
//#include <handlegraph/path_handle_graph.hpp>
#include <handlegraph/path_position_handle_graph.hpp>
//#include <handlegraph/mutable_handle_graph.hpp>
//#include <handlegraph/mutable_path_handle_graph.hpp>
//#include <handlegraph/mutable_path_mutable_handle_graph.hpp>
//#include <handlegraph/deletable_handle_graph.hpp>
//#include <handlegraph/mutable_path_deletable_handle_graph.hpp>
#include "handlegraph/types.hpp"
#include "handlegraph/iteratee.hpp"
#include "handlegraph/util.hpp"
#include "handlegraph/handle_graph.hpp"
#include "handlegraph/path_position_handle_graph.hpp"

#include "mmmultimap.hpp"

Expand Down