1.1.0 dev

.github/workflows/build-and-test.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   check-build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     container:
       image: traviswheelerlab/ultra-build
       volumes:
@@ -14,17 +14,17 @@ jobs:
       - run: cmake . && make
 
   check-examples:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     container:
       image: traviswheelerlab/ultra-build
       volumes:
         - ${{ github.workspace }}:/code
     steps:
       - uses: actions/checkout@v3
       - run: cmake . && make examples
-      
+
   check-format:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     container:
       image: traviswheelerlab/ultra-build
       volumes:

CMakeLists.txt

@@ -4,25 +4,25 @@ project(
         HOMEPAGE_URL https://github.com/TravisWheelerLab/ULTRA
 )
 
+# By default we do NOT build the standalone ULTRA library
+option(BUILD_ULTRA_LIB "Also build ULTRA as a standalone library" OFF)
 
+# Default to Release if no build type is set
 if (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE STREQUAL "")
     message(STATUS "Setting CMAKE_BUILD_TYPE=Release")
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 endif()
 
-if(NOT CMAKE_BUILD_TYPE STREQUAL "Release")
+# Add a debug flag when not in Release
+if (NOT CMAKE_BUILD_TYPE STREQUAL "Release")
     add_definitions(-DDEBUG_PRAGMA=1)
 endif()
 
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-set(
-        LIB_CPP_FILES
-)
-set(
-        HPP_FILES
-
+# Header files (for installation / PUBLIC_HEADER)
+set(HPP_FILES
         src/FASTAReader.hpp
         src/FileReader.hpp
         src/SequenceWindow.hpp
@@ -39,10 +39,10 @@ set(
         src/RepeatSplitter.hpp
         src/cli.hpp
         src/mask.hpp
-)
-set(
-        CPP_FILES
+        )
 
+# All source files
+set(CPP_FILES
         src/FASTAReader.cpp
         src/FileReader.cpp
         src/SequenceWindow.cpp
@@ -63,21 +63,46 @@ set(
 
 find_package(Threads REQUIRED)
 
-add_executable(
-        ultra
+# LIB_SOURCES = everything except main.cpp
+set(LIB_SOURCES ${CPP_FILES})
+list(REMOVE_ITEM LIB_SOURCES src/main.cpp)
 
-        ${LIB_CPP_FILES}
-        ${CPP_FILES}
-)
-target_link_libraries(ultra PRIVATE Threads::Threads)
+# 1) Build static library only if requested
+if (BUILD_ULTRA_LIB)
+    add_library(ultra_core STATIC ${LIB_SOURCES})
+    target_include_directories(ultra_core
+            PUBLIC ${CMAKE_SOURCE_DIR}/src
+            )
+    target_link_libraries(ultra_core
+            PUBLIC Threads::Threads
+            )
+
+    install(
+            TARGETS ultra_core
+            ARCHIVE DESTINATION lib
+            PUBLIC_HEADER DESTINATION include
+    )
+endif()
+
+# 2) Build the CLI executable
+if (BUILD_ULTRA_LIB)
+    # Link only main.cpp against ultra_core
+    add_executable(ultra src/main.cpp)
+    target_link_libraries(ultra PRIVATE ultra_core)
+else()
+    # Monolithic: compile everything into the exe
+    add_executable(ultra ${CPP_FILES})
+    target_link_libraries(ultra PRIVATE Threads::Threads)
+endif()
 
-target_include_directories(ultra SYSTEM PRIVATE ${CMAKE_SOURCE_DIR}/lib)
+target_include_directories(ultra PRIVATE ${CMAKE_SOURCE_DIR}/src)
 
-install(TARGETS ultra RUNTIME)
+install(TARGETS ultra RUNTIME DESTINATION bin)
 
+# Optional examples target
 add_custom_target(
         examples
-        COMMAND examples/run-all.sh
+        COMMAND /usr/bin/env sh examples/run-all.sh
         VERBATIM
 )
 add_dependencies(examples ultra)

examples/Makefile

@@ -0,0 +1,33 @@
+# examples/Makefile — build the ULTRA example program
+
+# C++ compiler and flags
+CXX        := g++
+CXXFLAGS   := -std=c++11 -Wall -I../src
+
+# Path to the ULTRA static library
+ULTRA_LIB  := ../build/libultra_core.a
+
+# Libraries to link against
+LDLIBS     := $(ULTRA_LIB) -pthread
+
+# Your example source & target
+SRC        := library_example.cpp
+OBJ        := $(SRC:.cpp=.o)
+TARGET     := library_example
+
+# Default target: build the example executable
+all: $(TARGET)
+
+# Link step
+$(TARGET): $(OBJ)
+	$(CXX) $(CXXFLAGS) $^ -o $@ $(LDLIBS)
+
+# Compile step
+%.o: %.cpp
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+
+# Clean up build artifacts
+clean:
+	rm -f $(OBJ) $(TARGET)
+
+.PHONY: all clean

examples/library_example.cpp

@@ -0,0 +1,70 @@
+//
+// Created by Daniel Olson on 5/5/25.
+//
+#include <cstdio>
+#include <ultra.hpp>
+#include <cli.hpp>
+
+int main() {
+  printf("Note that the Makefile is currently linking against ULTRA/build/libultra_core.a\n");
+  printf("   and is using ULTRA/src/ as the source of ULTRA header files.\n");
+  printf("The location of the ULTRA lib and header files will need to be adjusted in real use-cases.\n\n\n");
+
+  printf("Starting test of library.\n");
+
+
+  // These are the settings we will use with ULTRA
+  Settings *settings = new Settings();
+  settings->run_without_reader = true; // This must be set to true when using as lib
+  settings->window_size = 1000000; // window size should be equal to the largest sequence you will analyze
+  settings->overlap = 0; // overlap should be turned off
+
+
+  // We can also pass in an argument string to settings like so:
+  int argc;
+  char **argv;
+  std::string arg_string = "-p 25 -i 3 -d 3";
+  string_to_args(arg_string, argc, argv);
+
+  settings->prepare_settings(); // This should be called before running settings->parse_input()
+  if (!settings->parse_input(argc, (const char**)argv)) {
+    exit(0);
+  }
+
+  // Finally, we call settings->assign_settings()
+  settings->assign_settings();
+
+  // We create a reusable ULTRA object
+  auto ultra = new Ultra(settings);
+  // We can find repeats in a C++ string using "FindRepeatsInString(std::string)"
+
+  printf("Finding repeats in string ``aaaaaaaaaaaaaaaaaaaaaaaaaa''\n");
+  auto repeats = ultra->FindRepeatsInString("aaaaaaaaaaaaaaaaaaaaaaaaaa");
+
+  printf("Start Length Pattern\n");
+  for (int i= 0; i < repeats->size(); ++i) {
+    auto r = repeats->at(i);
+    printf("%lu %lu %i %s\n", r->windowStart, r->repeatLength, r->repeatPeriod, r->GetConsensus().c_str());
+    delete r; // We are in charge of the memory management of the repeats returned by FindRepeatsInString
+  }
+
+  delete repeats; // We are also in charge of the memory for the repeat array itself
+  printf("---------\n");
+
+
+  printf("Finding repeats in string ``aggtaaggtaaggtaaggtaaggtaagcggtataacatacagatctgactactactactactactactactactac''\n");
+  repeats = ultra->FindRepeatsInString("aggtaaggtaaggtaaggtaaggtaagcggtataacatacagatctgactactactactactactactactactac");
+  printf("Start Length Pattern\n");
+  for (int i= 0; i < repeats->size(); ++i) {
+    auto r = repeats->at(i);
+    printf("%lu %lu %i %s\n", r->windowStart, r->repeatLength, r->repeatPeriod, r->GetConsensus().c_str());
+    delete r;
+  }
+
+  delete repeats;
+  printf("---------\n");
+
+  printf("All positions reported are 0 indexed.\n");
+
+  return 0;
+}

examples/run-all.sh

@@ -16,3 +16,4 @@ run_one() {
 
 run_one examples/example_1.fa
 run_one examples/example_2.fa
+run_one examples/example_3.fa

src/BEDFileWriter.cpp

@@ -7,7 +7,10 @@
 #include "ultra.hpp"
 #include <algorithm>
 #include <iostream>
-void BEDFileWriter::InitializeWriter(Ultra *ultra, FILE *out_file) { owner = ultra; out=out_file; }
+void BEDFileWriter::InitializeWriter(Ultra *ultra, FILE *out_file) {
+  owner = ultra;
+  out = out_file;
+}
 
 void BEDFileWriter::WriteRepeat(RepeatRegion *repeat) {
 
@@ -35,7 +38,8 @@ void BEDFileWriter::WriteRepeat(RepeatRegion *repeat) {
   // We need to decide what to do with the overall sequence
 
   std::string rep_con = std::to_string(repeat->repeatPeriod);
-  if (owner->settings->max_consensus_period >= repeat->repeatPeriod && !repeat->string_consensus.empty())
+  if (owner->settings->max_consensus_period >= repeat->repeatPeriod &&
+      !repeat->string_consensus.empty())
     rep_con = repeat->string_consensus;
 
   fprintf(out, "\t%s\n", rep_con.c_str());

src/FASTAReader.cpp

@@ -130,7 +130,6 @@ bool FASTAReader::ReadWindow(SequenceWindow *window) {
   window->PrepareWindow(sequenceName, sequenceID, symbolsReadInSeq,
                         overlapLength);
 
-
   if (overlapLength > 0)
     window->CopyOverlap(overlapBuffer);
 
@@ -188,7 +187,6 @@ bool FASTAReader::ReadWindow(SequenceWindow *window) {
 
   window->readID = readID++;
 
-
   return true;
 }
 

src/FASTAReader.hpp

@@ -45,15 +45,15 @@ class FASTAReader {
   double C_pctg;
   double G_pctg;
 
-  symbol *overlapBuffer;          //    = NULL;
-  unsigned long overlapLength = 0;    //    = 0;
+  symbol *overlapBuffer;           //    = NULL;
+  unsigned long overlapLength = 0; //    = 0;
 
-  std::string sequenceName = "";       // = "";
+  std::string sequenceName = "";      // = "";
   unsigned long sequenceID = 0;       // = 0;
   unsigned long readID = 0;           // = 0; // read id's may not be contiguous
   unsigned long symbolsReadInSeq = 0; // = 0;
 
-  bool doneReadingFile;           //  = false;
+  bool doneReadingFile; //  = false;
   bool isReading;
 
   bool CopyOverlapBufferFromWindow(SequenceWindow *window,

src/FileReader.cpp

@@ -36,7 +36,6 @@ FileReader::~FileReader() {
     delete fastaReader;
     fastaReader = nullptr;
   }
-
 }
 
 SequenceWindow *FileReader::GetReadyWindow() {

src/FileReader.hpp

@@ -17,7 +17,6 @@ class FileReader {
   unsigned long maxSeqLength;
   unsigned long maxOverlapLength;
 
-
   bool multithread = true;
   file_type format = UNKNOWN;
 

src/JSONFileWriter.cpp

@@ -79,8 +79,7 @@ void JSONFileWriter::WriteRepeat(RepeatRegion *repeat) {
 
   ++this->repeatsOutput;
 
-  fprintf(out, "{\"SequenceName\": \"%s\"",
-          repeat->sequenceName.c_str());
+  fprintf(out, "{\"SequenceName\": \"%s\"", repeat->sequenceName.c_str());
 
   this->OutputJSONKeyValue("Start", std::to_string(repeat->sequenceStart));
   this->OutputJSONKeyValue("Length", std::to_string(repeat->repeatLength));
@@ -91,9 +90,10 @@ void JSONFileWriter::WriteRepeat(RepeatRegion *repeat) {
     this->OutputJSONKeyValue("PVal", std::to_string(pval));
   }
 
-
   if (owner->settings->show_counts) {
-    auto copies = (repeat->repeatLength - repeat->insertions + repeat->deletions) / repeat->repeatPeriod;
+    auto copies =
+        (repeat->repeatLength - repeat->insertions + repeat->deletions) /
+        repeat->repeatPeriod;
     this->OutputJSONKeyValue("Copies", std::to_string(copies));
     this->OutputJSONKeyValue("Substitutions",
                              std::to_string(repeat->mismatches));

src/RepeatSplitter.cpp

@@ -423,7 +423,6 @@ void ValidateSplits(std::vector<std::string> *consensi,
                             join_threshold)) {
       consensi->at(i) = consensi->at(i - 1);
       splits->at(i - 1) = -1;
-
     }
   }
 }

src/SequenceWindow.cpp

@@ -32,7 +32,8 @@ void SequenceWindow::PrepareWindow(std::string seqName, unsigned long sid,
   }
 }
 
-long long SequenceWindow::ReadLine(std::string line, long long place, unsigned long long &total_seq_length) {
+long long SequenceWindow::ReadLine(std::string line, long long place,
+                                   unsigned long long &total_seq_length) {
   // printf ("(mem: %llx overlap:%llx newseq: %llx, length: %llu, place %llu)
   // Reading line: %s\n", (unsigned long)seqMem, (unsigned long)overlapSeq,
   // (unsigned long)newSeq, length, place,  line.c_str());
@@ -156,7 +157,7 @@ bool CompareSequenceWindows::operator()(SequenceWindow *lhs,
 }
 
 void ShuffleSequenceWindow(SequenceWindow *window) {
-  std::random_device rd;  // a seed source for the random number engine
+  std::random_device rd; // a seed source for the random number engine
   std::mt19937 gen(rd());
   std::uniform_int_distribution<unsigned long long> dist;
   for (unsigned long long i = 0; i < window->length; ++i) {

src/SequenceWindow.hpp

@@ -44,7 +44,8 @@ class SequenceWindow {
 
   // ReadLine() returns how much of line was read
   // and will returns -1 if the line is a new sequence
-  long long ReadLine(std::string line, long long place, unsigned long long &total_seq_length);
+  long long ReadLine(std::string line, long long place,
+                     unsigned long long &total_seq_length);
   void CopyOverlap(symbol *b);
   void CalculateSymbolFrequencies();