From b8d5cb18ec6f7b12b77c43550129997cdc675e88 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sun, 10 Aug 2025 17:48:59 -0700
Subject: [PATCH 1/2] src/radmeth/radmeth.cpp: fixing things that got messed up
 in previous commit

---
 src/radmeth/radmeth.cpp | 37 ++++++++++++++++++++++++++-----------
 1 file changed, 26 insertions(+), 11 deletions(-)

diff --git a/src/radmeth/radmeth.cpp b/src/radmeth/radmeth.cpp
index e4a89aa3..97ea9ad7 100644
--- a/src/radmeth/radmeth.cpp
+++ b/src/radmeth/radmeth.cpp
@@ -37,20 +37,25 @@
 #include <vector>
 
 struct file_progress {
-  double one_hundred_over_filesize{};
+  double one_thousand_over_filesize{};
   std::size_t prev_offset{};
   explicit file_progress(const std::string &filename) :
-    one_hundred_over_filesize{100.0 / std::filesystem::file_size(filename)} {}
+    one_thousand_over_filesize{1000.0 / std::filesystem::file_size(filename)} {}
   void
   operator()(std::ifstream &in) {
     const std::size_t curr_offset =
-      in.eof() ? 100 : in.tellg() * one_hundred_over_filesize;
+      in.eof() ? 1000 : in.tellg() * one_thousand_over_filesize;
     if (curr_offset <= prev_offset)
       return;
-    std::cerr << "\r[progress: " << std::setw(3) << curr_offset
-              << (curr_offset == 100 ? "%]\n" : "%]");
-    prev_offset = (curr_offset == 100) ? std::numeric_limits<std::size_t>::max()
-                                       : curr_offset;
+    std::ios old_state(nullptr);
+    old_state.copyfmt(std::cerr);
+    std::cerr << "\r[progress: " << std::setw(5) << std::fixed
+              << std::setprecision(1) << (curr_offset / 10.0)
+              << (curr_offset == 1000 ? "%]\n" : "%]");
+    std::cerr.copyfmt(old_state);
+    prev_offset = (curr_offset == 1000)
+                    ? std::numeric_limits<std::size_t>::max()
+                    : curr_offset;
   }
 };
 
@@ -162,6 +167,9 @@ drop_idx(const std::vector<double> &v, const std::size_t idx_to_drop) {
   return u;
 }
 
+/// ADS: this function is not currently used, as the threads do not operate in
+/// "chunks"
+/*
 static inline void
 get_chunk_bounds(const std::uint32_t n_elements, const std::uint32_t n_chunks,
                  std::vector<std::pair<std::uint32_t, std::uint32_t>> &chunks) {
@@ -175,6 +183,7 @@ get_chunk_bounds(const std::uint32_t n_elements, const std::uint32_t n_chunks,
     block_start = block_end;
   }
 }
+*/
 
 static void
 radmeth(const bool show_progress, const bool more_na_info,
@@ -224,7 +233,7 @@ that the design matrix and the proportion table are correctly formatted.
   std::vector<Regression> alt_models(n_threads, alt_model);
   std::vector<Regression> null_models(n_threads, null_model);
 
-  std::vector<std::pair<std::uint32_t, std::uint32_t>> chunks(n_threads);
+  // std::vector<std::pair<std::uint32_t, std::uint32_t>> chunks(n_threads);
 
   // Iterate over rows in the file and do llr test on proportions from
   // each. Do this in sets of rows to avoid having to spawn too many threads.
@@ -235,15 +244,21 @@ that the design matrix and the proportion table are correctly formatted.
     if (n_lines == 0)
       break;
 
-    get_chunk_bounds(n_lines, n_threads, chunks);
+    /// ADS: chunks not used
+    // get_chunk_bounds(n_lines, n_threads, chunks);
 
     std::vector<std::thread> threads;
     for (auto thread_id = 0u; thread_id < n_threads; ++thread_id) {
       threads.emplace_back([&, thread_id] {
-        const auto &[chunk_beg, chunk_end] = chunks[thread_id];
+        /// ADS: chunks not used
+        // const auto &[chunk_beg, chunk_end] = chunks[thread_id];
         auto &t_alt_model = alt_models[thread_id];
         auto &t_null_model = null_models[thread_id];
-        for (auto b = chunk_beg; b != chunk_end; ++b) {
+        /// ADS: chunks not used
+        // for (auto b = chunk_beg; b != chunk_end; ++b) {
+        for (auto b = 0u; b < n_lines; ++b) {
+          if (b % n_threads != thread_id)
+            continue;
           t_alt_model.props.parse(lines[b]);
           if (t_alt_model.props_size() != n_samples)
             throw std::runtime_error("found row with wrong number of columns");

From 0204135f231c2054c56f888b97562ade99fadd29 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sun, 10 Aug 2025 17:49:12 -0700
Subject: [PATCH 2/2] src/radmeth/radmeth_optimize.cpp: fixing things that got
 messed up in previous commit

---
 src/radmeth/radmeth_optimize.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/radmeth/radmeth_optimize.cpp b/src/radmeth/radmeth_optimize.cpp
index 5d103c6f..4839c229 100644
--- a/src/radmeth/radmeth_optimize.cpp
+++ b/src/radmeth/radmeth_optimize.cpp
@@ -168,6 +168,7 @@ static void
 neg_gradient(const gsl_vector *params, void *object, gsl_vector *output) {
   auto reg = static_cast<Regression *>(object);
   gradient(params, *reg, output);
+  gsl_vector_scale(output, -1.0);
 }
 
 static void