style: Run treefmt

crates.nix

@@ -1,9 +1,5 @@
 {...}: {
-  perSystem = {
-    pkgs,
-    config,
-    ...
-  }: let
+  perSystem = {pkgs, ...}: let
     cargoToml = builtins.fromTOML (builtins.readFile ./Cargo.toml);
     crateName = cargoToml.package.name;
   in {

doc/cli-output.md

@@ -1,4 +1,3 @@
-
 ```
 dragenos -r <reference> -b <base calls> [optional arguments]
 
@@ -195,4 +194,4 @@ Command line options:
 Failed to parse the options: /build/i5zj4f8yjlk2spizc3krc2x4k1yqkvz1-source/src/lib/options/DragenOsOptions.cpp(335): Throw in function postProcess
 Dynamic exception type: boost::wrapexcept<dragenos::common::InvalidOptionException>
 std::exception::what: fastq-file1 or bam-input must point to an existing fastq file
-```
+```

doc/refactor.md

@@ -2,7 +2,6 @@
 
 Ran `config.mk` through chatgpt4
 
-
 ## Refactoring Explanation:
 
 1. The checks for certain environment variables and command-line parameters (like `GTEST_INCLUDEDIR`, `GTEST_LIBRARYDIR`, `BOOST_INCLUDEDIR`, `BOOST_LIBRARYDIR`) are repeated, which can be refactored into a function-like macro for reusability.
@@ -134,7 +133,7 @@ GTEST_LDFLAGS+=-lgtest_main -lgtest
 
 sources := $(wildcard $(DRAGEN_OS_SRC_DIR)/*.cpp)
 programs := $(sources:$(DRAGEN_OS_SRC_DIR)/%.cpp=%)
-``` 
+```
 
 Diff:
 Given the amount of code and the complexity of the original file, it would be impractical to display all the exact diffs here. However, applying the above refactoring suggestions would result in removal of commented code blocks, consolidation of repeated checks into function-macros, and cleanliness and clarity in variable assignments and conditionals.

doc/usage.md

@@ -25,4 +25,3 @@ Or directly to a file :
 ## Align single-end reads :
 
     dragen-os -r /home/data/reference/ -1 reads_1.fastq.gz  >  result.sam
-

docs/rust-notes.md

@@ -1,2 +1 @@
 https://github.com/markschl/seq_io
-

docs/zig-notes.md

@@ -1,3 +1,2 @@
 https://github.com/blark/mmdvmhost-zig/blob/main/build.zig
 https://zig.news/kristoff/compile-a-c-c-project-with-zig-368j
-

src/include/align/VectorSmithWaterman.hpp

@@ -66,10 +66,7 @@ class VectorSmithWaterman {
 #endif
   }
 
-  ~VectorSmithWaterman()
-  {
-    free(sswScoringMat_);
-  }
+  ~VectorSmithWaterman() { free(sswScoringMat_); }
 
   uint16_t align(
       const unsigned char* queryBegin,

src/include/common/Threads.hpp

@@ -109,7 +109,7 @@ class BasicThreadPool {
     {
       return os << "Executor(" << e.maxThreads_ << "mt," << e.threadsIn_ << "ti," << e.complete_ << "c)";
     }
-  } * head_, *tail_;
+  } *                     head_, *tail_;
   static std::mutex       mutex_;
   std::condition_variable stateChangedCondition_;
 

src/include/reference/ReferenceSequence.hpp

@@ -199,14 +199,8 @@ class ReferenceSequence {
     return getRcBaseNoCheck(position);
   }
 
-  const unsigned char* getData() const
-  {
-    return data_;
-  }
-  size_t getSize() const
-  {
-    return size_;
-  }
+  const unsigned char* getData() const { return data_; }
+  size_t               getSize() const { return size_; }
   /// decode 4 bits into AIUPAC character using only 4 LSB
   static char decodeBase(unsigned char base);
   /// translate into 2 bits encoding using only 4 LSB

src/lib/common/SystemCompatibility.cpp

@@ -323,7 +323,7 @@ int64_t clock()
 
 bool isLittleEndian()
 {
-  const uint64_t v = 0x0706050403020100;
+  const uint64_t             v = 0x0706050403020100;
   const unsigned char* const p = reinterpret_cast<const unsigned char*>(&v);
   for (unsigned i = 0; i < sizeof(v); ++i) {
     if (p[i] != i) {
@@ -354,7 +354,7 @@ uint64_t getFileSize(const PathCharType* filePath)
 boost::filesystem::path getModuleFileName()
 {
   char szBuffer[10240];
-  int readBytes = readlink("/proc/self/exe", szBuffer, sizeof(szBuffer));
+  int  readBytes = readlink("/proc/self/exe", szBuffer, sizeof(szBuffer));
   DRAGEN_OS_ASSERT_MSG(-1 != readBytes, "TODO: handle the readlink error: " << errno);
   // readlink does not zero-terminate the string.
   szBuffer[readBytes] = 0;

src/lib/reference/ReferenceDir.cpp

@@ -53,7 +53,7 @@ typename ReferenceDir7::UcharPtr ReferenceDir7::ReadFileIntoBuffer(
   size = file.tellg();
   file.seekg(0, file.beg);
 
-  UcharPtr bufPtr(new uint8_t[size], [](uint8_t* p) -> void { delete[](p); });
+  UcharPtr bufPtr(new uint8_t[size], [](uint8_t* p) -> void { delete[] (p); });
   file.read(reinterpret_cast<char*>(bufPtr.get()), size);
   if (!file) {
     //    THROW(DragenException, "Could not load reference - could not read ", path);

src/lib/reference/tests/integration/ExtendTableIntervalGtest.cpp

@@ -41,7 +41,7 @@ TEST(ExtendTableInterval, SetOfTwo)
   uint64_t  s4[]     = {0x7bf9df58fa123456, 0x7bf9fedcfb987654};
   uint64_t* ss[]     = {s1, s2, s3, s4};
   uint32_t  esl[][3] = {
-       {0, 0x56987654, 0x1234}, {0x12, 0x56987654, 0x34}, {0, 0x56, 0x34987654}, {0, 0x123456, 0x987654}};
+      {0, 0x56987654, 0x1234}, {0x12, 0x56987654, 0x34}, {0, 0x56, 0x34987654}, {0, 0x123456, 0x987654}};
   for (unsigned i = 0; 4 > i; ++i) {
     const auto begin = reinterpret_cast<const HashRecord*>(ss[i]);
     const auto end   = begin + 2;
@@ -94,7 +94,7 @@ TEST(ExtendTableInterval, SetOfThree)
   uint64_t  s5[]    = {0xc851b149f900001a, 0xc851b148fabb10ae, 0xc851b14afb01f3b0};
   uint64_t* ss[]    = {s1, s2, s3, s4, s5};
   uint32_t  sl[][2] = {
-       {5777464, 92356}, {4231852, 80514}, {0x27c4fc2, 106658}, {0x1b46391e, 96576}, {0x1abb10ae, 127920}};
+      {5777464, 92356}, {4231852, 80514}, {0x27c4fc2, 106658}, {0x1b46391e, 96576}, {0x1abb10ae, 127920}};
   for (unsigned i = 0; 5 > i; ++i) {
     const auto begin = reinterpret_cast<const HashRecord*>(ss[i]);
     const auto end   = begin + 3;

todo.org

@@ -3,7 +3,8 @@
 https://crates.io/crates/clap_mangen
 
 * Build System
-** TODO Add treefmt back in
+** DONE Add treefmt back in
+CLOSED: [2024-06-25 Tue 12:17]
 ** DONE Use https://flake.parts/ again
 CLOSED: [2024-06-25 Tue 12:15]
 ** TODO Use build.zig