[med-svn] [Git][med-team/bifrost][master] 7 commits: Source-only upload
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jan 5 08:20:56 GMT 2024
Andreas Tille pushed to branch master at Debian Med / bifrost
Commits:
38b68b7c by Andreas Tille at 2024-01-05T09:11:32+01:00
Source-only upload
- - - - -
8b0f7657 by Andreas Tille at 2024-01-05T09:12:14+01:00
routine-update: New upstream version
- - - - -
225683eb by Andreas Tille at 2024-01-05T09:12:15+01:00
New upstream version 1.3.1
- - - - -
508bf49d by Andreas Tille at 2024-01-05T09:12:15+01:00
Update upstream source from tag 'upstream/1.3.1'
Update to upstream version '1.3.1'
with Debian dir 0e381fd3758d7f4b5b6d4b82e72a05a98430ab00
- - - - -
5d99331d by Andreas Tille at 2024-01-05T09:12:23+01:00
routine-update: Remove trailing whitespace in debian/copyright
- - - - -
d673217d by Andreas Tille at 2024-01-05T09:12:49+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
b16203ac by Andreas Tille at 2024-01-05T09:16:07+01:00
routine-update: Ready to upload to unstable
- - - - -
11 changed files:
- CMakeLists.txt
- Changelog.md
- debian/changelog
- debian/copyright
- debian/upstream/metadata
- src/Bifrost.cpp
- src/ColorSet.cpp
- src/ColoredCDBG.hpp
- src/ColoredCDBG.tcc
- src/CompactedDBG.hpp
- src/strict_fstream.hpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -1,6 +1,7 @@
cmake_minimum_required(VERSION 2.8.12)
-project(Bifrost)
+project(Bifrost C CXX)
+find_package(Threads REQUIRED)
# To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
@@ -14,8 +15,17 @@ SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+set(CMAKE_MACOSX_RPATH 1)
+
set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
+if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+ message("Disabling AVX2 instructions on arm64")
+ set(ENABLE_AVX2 "OFF")
+ set(COMPILATION_ARCH "OFF")
+endif(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+
+
if(COMPILATION_ARCH MATCHES "OFF")
message("Disabling native architecture compilation (including AVX2)")
else(COMPILATION_ARCH MATCHES "OFF")
=====================================
Changelog.md
=====================================
@@ -2,6 +2,8 @@
API only.
+* **17-11-2023**
+ * Class `ColoredCDBG` exposes the function `readGraph()` which enables to load/read the graph in a colored de Bruijn graph without associating any colors to the unitigs. This enables to later color the graph with any input sequences.
* **10-09-2023**
* Function `CompactedDBG()::search()` takes additional arguments:
* `get_nb_found_km`: boolean indicating whether to report in the output the number of found k-mers per query
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+bifrost (1.3.1-1) unstable; urgency=medium
+
+ * Source-only upload.
+ * New upstream version
+ * Remove trailing whitespace in debian/copyright (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Fri, 05 Jan 2024 09:14:39 +0100
+
bifrost (1.3.0-1) unstable; urgency=medium
* Initial release (Closes: #1055593)
=====================================
debian/copyright
=====================================
@@ -183,7 +183,7 @@ License: CC-BY-SA-3.0
Adaptation for the purpose of this License.
b. Collection means a collection of literary or artistic works, such as
encyclopedias and anthologies, or performances, phonograms or broadcasts,
- or other works or subject matter other than works listed in Section 1(f)
+ or other works or subject matter other than works listed in Section 1(f)
below, which, by reason of the selection and arrangement of their contents,
constitute intellectual creations, in which the Work is included in its
entirety in unmodified form along with one or more other contributions,
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/pmelsted/bifrost/issues
+Bug-Submit: https://github.com/pmelsted/bifrost/issues/new
Reference:
- Author: Guillaume Holley and Páll Melsted
Title: >
@@ -18,3 +20,4 @@ Registry:
Entry: bifrost
- Name: bio.tools
Entry: Bifrost
+Repository-Browse: https://github.com/pmelsted/bifrost
=====================================
src/Bifrost.cpp
=====================================
@@ -723,7 +723,7 @@ int main(int argc, char **argv){
else success = ccdbg.read(opt.filename_graph_in, opt.filename_index_in, opt.filename_colors_in, opt.nb_threads, opt.verbose);
if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.get_nb_found_km, opt.get_ratio_found_km,
- opt.inexact_search, opt.nb_threads, opt.verbose);
+ opt.inexact_search, opt.nb_threads, opt.verbose);
}
else {
=====================================
src/ColorSet.cpp
=====================================
@@ -1,3 +1,7 @@
+#if defined(__APPLE__)
+#include <unistd.h>
+#endif
+
#include "ColorSet.hpp"
UnitigColors::UnitigColors() : setBits(localBitVector) {}
=====================================
src/ColoredCDBG.hpp
=====================================
@@ -197,13 +197,13 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
ColoredCDBG& operator=(ColoredCDBG&& o);
/** Equality operator.
- * @return a boolean indicating if two compacted de Bruijn graphs have the same colored unitigs (does not
+ * @return a boolean indicating whether two compacted de Bruijn graphs have the same colored unitigs (does not
* compare the data associated with the unitigs).
*/
bool operator==(const ColoredCDBG& o) const;
/** Inequality operator.
- * @return a boolean indicating if two compacted de Bruijn graphs have different colored unitigs (does not
+ * @return a boolean indicating whether two compacted de Bruijn graphs have different colored unitigs (does not
* compare the data associated with the unitigs).
*/
inline bool operator!=(const ColoredCDBG& o) const;
@@ -229,14 +229,14 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
/** Build the Colored and compacted de Bruijn graph (only the unitigs).
* A call to ColoredCDBG::mapColors is required afterwards to map colors to unitigs.
* @param opt is a structure from which the members are parameters of this function. See CCDBG_Build_opt.
- * @return boolean indicating if the graph has been built successfully.
+ * @return boolean indicating whether the graph has been built successfully.
*/
bool buildGraph(const CCDBG_Build_opt& opt);
/** Map the colors to the unitigs. This is done by reading the input files and querying the graph.
* If a color filename is provided in opt.filename_colors_in, colors are loaded from that file instead.
* @param opt is a structure from which the members are parameters of this function. See CCDBG_Build_opt.
- * @return boolean indicating if the colors have been mapped successfully.
+ * @return boolean indicating whether the colors have been mapped successfully.
*/
bool buildColors(const CCDBG_Build_opt& opt);
@@ -248,11 +248,11 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* @param write_meta_file indicates if a graph meta file is written to disk. Graph meta files enable faster graph loading.
* @param compressed_output indicates if the output file is compressed.
* @param verbose is a boolean indicating if information message are printed during writing (true) or not (false).
- * @return a boolean indicating if the graph was successfully written.
+ * @return a boolean indicating whether the graph was successfully written.
*/
bool write(const string& prefix_output_fn, const size_t nb_threads = 1, const bool write_index_file = true, const bool compress_output = false, const bool verbose = false) const;
- /** Read a colored and compacted de Bruijn graph from disk. The graph (in GFA, FASTA or BFG format) must
+ /** Load a colored and compacted de Bruijn graph from disk. The graph (in GFA, FASTA or BFG format) must
* have been produced by Bifrost. By default, the function detects if an index file (BFI format) exists for the
* input graph and will use it to load the graph. Otherwise, reading the graph will be much slower
* than function read() with the index filename in input parameter.
@@ -260,21 +260,40 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* @param input_colors_fn is a string which is the prefix of the color filename to read
* @param nb_threads is the number of threads that can be used to read the graph and its colors from disk.
* @param verbose is a boolean indicating if information messages are printed during reading (true) or not (false).
- * @return a boolean indicating if the graph was successfully read.
+ * @return a boolean indicating whether the graph was successfully read.
*/
bool read(const string& input_graph_fn, const string& input_colors_fn, const size_t nb_threads = 1, const bool verbose = false);
- /** Read a colored and compacted de Bruijn graph from disk using an index file. The graph (in GFA, FASTA or BFG format)
- * must have been produced by Bifrost.
+ /** Load a colored and compacted de Bruijn graph from disk using an index file.
+ * The graph (in GFA, FASTA or BFG format) must have been produced by Bifrost.
* @param input_graph_fn is a string which is the prefix of the graph filename to read
* @param input_index_fn is a string which is the prefix of the index filename to read
* @param input_colors_fn is a string which is the prefix of the color filename to read
* @param nb_threads is the number of threads that can be used to read the graph and its colors from disk.
* @param verbose is a boolean indicating if information messages are printed during reading (true) or not (false).
- * @return a boolean indicating if the graph was successfully read.
+ * @return a boolean indicating whether the graph was successfully read.
*/
bool read(const string& input_graph_fn, const string& input_index_fn, const string& input_colors_fn, const size_t nb_threads = 1, const bool verbose = false);
+ /** Load a colored and compacted de Bruijn graph without its colors from disk.
+ * A call to ColoredCDBG::mapColors is required afterwards to map colors to unitigs.
+ * @param input_graph_fn is a string which is the prefix of the graph filename to read
+ * @param nb_threads is the number of threads that can be used to read the graph and its colors from disk.
+ * @param verbose is a boolean indicating if information messages are printed during reading (true) or not (false).
+ * @return a boolean indicating whether the graph was successfully read.
+ */
+ bool readGraph(const string& input_graph_fn, const size_t nb_threads = 1, const bool verbose = false);
+
+ /** Load a colored and compacted de Bruijn graph without its colors from disk using an index file.
+ * A call to ColoredCDBG::mapColors is required afterwards to map colors to unitigs.
+ * @param input_graph_fn is a string which is the prefix of the graph filename to read
+ * @param input_index_fn is a string which is the prefix of the index filename to read
+ * @param nb_threads is the number of threads that can be used to read the graph and its colors from disk.
+ * @param verbose is a boolean indicating if information messages are printed during reading (true) or not (false).
+ * @return a boolean indicating whether the graph was successfully read.
+ */
+ bool readGraph(const string& input_graph_fn, const string& input_index_fn, const size_t nb_threads = 1, const bool verbose = false);
+
/** Merge a colored and compacted de Bruijn graph.
* After merging, all unitigs and colors of the input graph have been added to and compacted with the current
* colored and compacted de Bruijn graph (this). If the unitigs of the input graph had data of type "MyUnitigData"
@@ -285,7 +304,7 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* @param o is a constant reference to the colored and compacted de Bruijn graph to merge.
* @param nb_threads is an integer indicating how many threads can be used during the merging.
* @param verbose is a boolean indicating if information messages must be printed during the execution of the function.
- * @return a boolean indicating if the graph has been successfully merged.
+ * @return a boolean indicating whether the graph has been successfully merged.
*/
bool merge(const ColoredCDBG& o, const size_t nb_threads = 1, const bool verbose = false);
@@ -301,7 +320,7 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* std::move(). After merging, the graph pointed by o is cleared.
* @param nb_threads is an integer indicating how many threads can be used during the merging.
* @param verbose is a boolean indicating if information messages must be printed during the execution of the function.
- * @return a boolean indicating if the graph has been successfully merged.
+ * @return a boolean indicating whether the graph has been successfully merged.
*/
bool merge(ColoredCDBG&& o, const size_t nb_threads = 1, const bool verbose = false);
@@ -313,7 +332,7 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* @param v is a constant reference to a vector of colored and compacted de Bruijn graphs to merge.
* @param nb_threads is an integer indicating how many threads can be used during the merging.
* @param verbose is a boolean indicating if information messages must be printed during the execution of the function.
- * @return a boolean indicating if the graphs have been successfully merged.
+ * @return a boolean indicating whether the graphs have been successfully merged.
*/
bool merge(const vector<ColoredCDBG>& v, const size_t nb_threads = 1, const bool verbose = false);
@@ -327,7 +346,7 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
* obtained using std::move(). After merging, the graphs in v are cleared.
* @param nb_threads is an integer indicating how many threads can be used during the merging.
* @param verbose is a boolean indicating if information messages must be printed during the execution of the function.
- * @return a boolean indicating if the graphs have been successfully merged.
+ * @return a boolean indicating whether the graphs have been successfully merged.
*/
bool merge(vector<ColoredCDBG>&& v, const size_t nb_threads = 1, const bool verbose = false);
=====================================
src/ColoredCDBG.tcc
=====================================
@@ -719,6 +719,115 @@ bool ColoredCDBG<U>::read(const string& input_graph_fn, const string& input_inde
return valid_input_files;
}
+template<typename U>
+bool ColoredCDBG<U>::readGraph(const string& input_graph_fn, const size_t nb_threads, const bool verbose) {
+
+ bool valid_input_files = true;
+
+ if (input_graph_fn.length() != 0){
+
+ if (check_file_exists(input_graph_fn)){
+
+ FILE* fp = fopen(input_graph_fn.c_str(), "r");
+
+ if (fp == NULL) {
+
+ cerr << "ColoredCDBG::readGraph(): Could not open input graph file " << input_graph_fn << endl;
+ valid_input_files = false;
+ }
+ else fclose(fp);
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): Input graph file " << input_graph_fn << " does not exist." << endl;
+ valid_input_files = false;
+ }
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): No input graph file provided." << endl;
+ valid_input_files = false;
+ }
+
+ if (valid_input_files){
+
+ if (verbose) cout << "ColoredCDBG::readGraph(): Reading graph." << endl;
+
+ invalid = !CompactedDBG<DataAccessor<U>, DataStorage<U>>::read(input_graph_fn, nb_threads, verbose);
+
+ if (invalid) return false; // Read graph
+ }
+
+ return valid_input_files;
+}
+
+template<typename U>
+bool ColoredCDBG<U>::readGraph(const string& input_graph_fn, const string& input_index_fn, const size_t nb_threads, const bool verbose) {
+
+ bool valid_input_files = true;
+
+ if (input_graph_fn.length() != 0){
+
+ if (check_file_exists(input_graph_fn)){
+
+ FILE* fp = fopen(input_graph_fn.c_str(), "r");
+
+ if (fp == NULL) {
+
+ cerr << "ColoredCDBG::readGraph(): Could not open input graph file " << input_graph_fn << endl;
+ valid_input_files = false;
+ }
+ else fclose(fp);
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): Input graph file " << input_graph_fn << " does not exist." << endl;
+ valid_input_files = false;
+ }
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): No input graph file provided." << endl;
+ valid_input_files = false;
+ }
+
+ if (input_index_fn.length() != 0){
+
+ if (check_file_exists(input_index_fn)){
+
+ FILE* fp = fopen(input_index_fn.c_str(), "rb");
+
+ if (fp == NULL) {
+
+ cerr << "ColoredCDBG::readGraph(): Could not open input index file " << input_index_fn << endl;
+ valid_input_files = false;
+ }
+ else fclose(fp);
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): Input index file " << input_index_fn << " does not exist." << endl;
+ valid_input_files = false;
+ }
+ }
+ else {
+
+ cerr << "ColoredCDBG::readGraph(): No input index file provided." << endl;
+ valid_input_files = false;
+ }
+
+ if (valid_input_files){
+
+ if (verbose) cout << "ColoredCDBG::readGraph(): Reading graph." << endl;
+
+ invalid = !CompactedDBG<DataAccessor<U>, DataStorage<U>>::read(input_graph_fn, input_index_fn, nb_threads, verbose);
+
+ if (invalid) return false; // Read graph
+ }
+
+ return valid_input_files;
+}
+
template<typename U>
void ColoredCDBG<U>::initUnitigColors(const CCDBG_Build_opt& opt, const size_t max_nb_hash){
@@ -1421,7 +1530,7 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
if (get_nb_found_km && get_ratio_found_km){
- cerr << "ColoredCDBG::search(): Cannot output at once the number of found k-mers and the ratio of found k-mers." << endl;
+ cerr << "ColoredCDBG::search(): Cannot output number of found k-mers and ratio of found k-mers together." << endl;
return false;
}
@@ -1538,7 +1647,6 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
else {
const Kmer head = um.getUnitigTail().twin();
- const size_t max_pos_um = um.dist + um.len - 1;
it = s_um.find({pos_query, {head, um.dist}});
@@ -1569,6 +1677,8 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
if (inexact_search){
+ const size_t max_pos_um = um.dist + um.len - 1;
+
for (; it_uc != it_uc_end; ++it_uc) color_occ_r[it_uc.getColorID()].add(max_pos_um - it_uc.getKmerPosition() + p.first);
}
else {
@@ -1593,31 +1703,40 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
if (inexact_search){
- size_t nb_color_pres = 0;
+ if (!get_nb_found_km && !get_ratio_found_km) {
- for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
+ size_t nb_color_pres = 0;
- if (nb_color_pres == nb_colors) return;
+ for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
+
+ if (nb_color_pres == nb_colors) return;
+ }
const vector<pair<size_t, const_UnitigColorMap<U>>> v_um_d = this->searchSequence(query, false, false, true, false, false);
processCounts(v_um_d, color_occ_r, color_occ_u); // Extract k-mer occurrences for each color
- nb_color_pres = 0;
+ if (!get_nb_found_km && !get_ratio_found_km) {
+
+ size_t nb_color_pres = 0;
- for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
+ for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
- if (nb_color_pres == nb_colors) return;
+ if (nb_color_pres == nb_colors) return;
+ }
const vector<pair<size_t, const_UnitigColorMap<U>>> v_um_m = this->searchSequence(query, false, false, false, true, false);
processCounts(v_um_m, color_occ_r, color_occ_u); // Extract k-mer occurrences for each color
- nb_color_pres = 0;
+ if (!get_nb_found_km && !get_ratio_found_km) {
+
+ size_t nb_color_pres = 0;
- for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
+ for (size_t j = 0; j < nb_colors; ++j) nb_color_pres += (color_occ_u[j] >= nb_km_min);
- if (nb_color_pres == nb_colors) return;
+ if (nb_color_pres == nb_colors) return;
+ }
const vector<pair<size_t, const_UnitigColorMap<U>>> v_um_i = this->searchSequence(query, false, true, false, false, false);
@@ -1735,7 +1854,9 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
for (size_t i = 0; i < nb_colors; ++i) {
color_query_out += '\t';
- color_query_out += to_string(get_ratio_found_km ? color_occ[i] : (static_cast<double>(color_occ[i]) / static_cast<double>(nb_km_query)));
+
+ if (get_nb_found_km) color_query_out += to_string(color_occ[i]);
+ else color_query_out += to_string(static_cast<double>(color_occ[i]) / static_cast<double>(nb_km_query));
}
const size_t l_color_query_out = color_query_out.length();
@@ -1772,7 +1893,9 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
for (size_t i = 0; i < nb_colors; ++i) {
color_query_out += '\t';
- color_query_out += to_string(get_ratio_found_km ? color_occ[i] : (static_cast<double>(color_occ[i]) / static_cast<double>(nb_km_query)));
+
+ if (get_nb_found_km) color_query_out += to_string(color_occ[i]);
+ else color_query_out += to_string(static_cast<double>(color_occ[i]) / static_cast<double>(nb_km_query));
}
const size_t l_color_query_out = color_query_out.length();
@@ -1941,7 +2064,7 @@ bool ColoredCDBG<U>::search(const vector<string>& query_filenames, const string&
for (auto& c : buffers_seq[i]) c &= 0xDF;
- if (get_nb_found_km){
+ if (get_nb_found_km || get_ratio_found_km){
searchQuery(buffers_seq[i], color_occ_r, color_occ_u, nb_km_query);
writeOutQuantMutex(buffers_name[i].c_str(), buffers_name[i].length(), nb_km_query, color_occ_u, buffer_res, pos_buffer_out, mutex_file_out);
=====================================
src/CompactedDBG.hpp
=====================================
@@ -164,7 +164,6 @@ struct CDBG_Build_opt {
bool get_nb_found_km;
bool get_ratio_found_km;
-
bool writeIndexFile;
double ratio_kmers;
=====================================
src/strict_fstream.hpp
=====================================
@@ -64,7 +64,7 @@ static std::string strerror()
} else {
return "Unknown error (" + std::to_string(err_num) + ")";
}
-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__)
+#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__)
// XSI-compliant strerror_r()
const int err_num = errno; // See above
if (strerror_r(err_num, buff.data(), buff.size()) == 0) {
View it on GitLab: https://salsa.debian.org/med-team/bifrost/-/compare/ea7c397729456fc7d79a900fa80d66a7f9e12310...b16203ac35d4d24b3ed5a8ded57de879f745e911
--
View it on GitLab: https://salsa.debian.org/med-team/bifrost/-/compare/ea7c397729456fc7d79a900fa80d66a7f9e12310...b16203ac35d4d24b3ed5a8ded57de879f745e911
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