From 144874ddad15e5bc4cdba5561c060e426c4bcaf5 Mon Sep 17 00:00:00 2001
From: jonathonl <jonathonl@users.noreply.github.com>
Date: Thu, 9 Nov 2023 15:23:08 -0500
Subject: [PATCH] Adds --min-ratio-behavior option to allow for skipping chunks
 with low number of target sites.

---
 src/main.cpp      | 9 ++++++++-
 src/prog_args.hpp | 8 ++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/main.cpp b/src/main.cpp
index 6069268..e6e7c12 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -80,7 +80,14 @@ class imputation
       float tar_ref_ratio = float(typed_only_reference_data.variant_size()) / float(full_reference_data.variant_size());
       std::cerr << "Typed sites to imputed sites ratio: " << tar_ref_ratio << " (" << typed_only_reference_data.variant_size() << "/" << full_reference_data.variant_size() << ")\n";
       if (tar_ref_ratio < args.min_ratio())
-        return std::cerr << "Error: not enough target variants are available to impute this chunk. The --min-ratio, --chunk, or --region options may need to be altered.\n", false;
+      {
+        std::cerr << (args.fail_min_ratio() ? "Error" : "Warning")  << ": not enough target variants are available to impute this chunk. The --min-ratio, --chunk, or --region options may need to be altered." << std::endl;
+        if (!args.fail_min_ratio())
+          std::cerr << "Warning: skipping chunk " << impute_region.chromosome() << ":" << impute_region.from() << "-" << impute_region.to() << std::endl;
+        if (args.fail_min_ratio())
+          return false;
+        return true; // skip
+      }
 
       if (target_only_sites.size())
       {
diff --git a/src/prog_args.hpp b/src/prog_args.hpp
index c433902..882c074 100644
--- a/src/prog_args.hpp
+++ b/src/prog_args.hpp
@@ -46,6 +46,7 @@ class prog_args : public getopt_wrapper
   bool compress_reference_ = false;
   bool pass_only_ = false;
   bool meta_ = false; // deprecated
+  bool fail_min_ratio_ = true;
   bool help_ = false;
   bool version_ = false;
 
@@ -81,6 +82,7 @@ class prog_args : public getopt_wrapper
   bool update_m3vcf() const { return update_m3vcf_; }
   bool compress_reference() const { return compress_reference_; }
   bool pass_only() const { return pass_only_; }
+  bool fail_min_ratio() const { return fail_min_ratio_; }
 
   prog_args() :
     getopt_wrapper(
@@ -106,6 +108,7 @@ class prog_args : public getopt_wrapper
         {"decay", required_argument, 0, '\x02', "Decay rate for dosages in flanking regions (default: disabled with 0)"},
         {"min-r2", required_argument, 0, '\x02', "Minimum estimated r-square for output variants"},
         {"min-ratio", required_argument, 0, '\x02', "Minimum ratio of number of target sites to reference sites (default: 0.00001)"},
+        {"min-ratio-behavior", required_argument, 0, '\x02', "Behavior for when --min-ratio is not met (\"skip\" or \"fail\"; default: fail)"}, // maybe add "warn"
         {"match-error", required_argument, 0, '\x02', "Error parameter for HMM match probabilities (default: 0.01)"},
         {"min-recom", required_argument, 0, '\x02', "Minimum recombination probability (default: 0.00001)"},
         {"prob-threshold", required_argument, 0, '\x02', "Probability threshold used for template selection"},
@@ -299,6 +302,11 @@ class prog_args : public getopt_wrapper
             min_ratio_ = std::min(1., std::max(0., std::atof(optarg ? optarg : "")));
             break;
           }
+          else if (long_opt_str == "min-ratio-behavior")
+          {
+            fail_min_ratio_ = std::string(optarg ? optarg : "") == "fail";
+            break;
+          }
           else if (long_opt_str == "match-error")
           {
             error_param_ = std::min(0.5, std::max(0., std::atof(optarg ? optarg : "")));