From 9835de1f30ef6fd251b48538c21db04477dd974f Mon Sep 17 00:00:00 2001
From: jonperdomo <jonperdomodb@gmail.com>
Date: Thu, 17 Oct 2024 15:14:16 -0400
Subject: [PATCH] CNV output updates

---
 src/cnv_caller.cpp | 2 +-
 src/sv_caller.cpp  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/cnv_caller.cpp b/src/cnv_caller.cpp
index 27fbab6f..73aa73c8 100644
--- a/src/cnv_caller.cpp
+++ b/src/cnv_caller.cpp
@@ -446,7 +446,7 @@ void CNVCaller::runCopyNumberPredictionChunk(std::string chr, std::map<SVCandida
             sv_snps.state_sequence = std::move(state_sequence);
 
             // Save the SV calls as a TSV file
-            std::string cnv_type_str = SVTypeString[cnv_type];
+            std::string cnv_type_str = SVTypeString[updated_sv_type];
             std::string sv_filename = this->input_data->getOutputDir() + "/" + cnv_type_str + "_" + chr + "_" + std::to_string((int) start_pos) + "-" + std::to_string((int) end_pos) + "_CIGAR.tsv";
             std::cout << "Saving SV CIGAR copy number predictions to " << sv_filename << "..." << std::endl;
             this->saveSVCopyNumberToTSV(sv_snps, sv_filename, chr, start_pos, end_pos, cnv_type_str, likelihood);
diff --git a/src/sv_caller.cpp b/src/sv_caller.cpp
index ead74f5f..acaae791 100644
--- a/src/sv_caller.cpp
+++ b/src/sv_caller.cpp
@@ -633,7 +633,7 @@ void SVCaller::detectSVsFromSplitReads(SVData& sv_calls, PrimaryMap& primary_map
                 // Determine which SV to keep based on HMM prediction likelihood
                 if (sv_list.size() == 1) {
                     // Just add the SV call
-                    std::cout << "Adding single SV call" << std::endl;
+                    // std::cout << "Adding single SV call" << std::endl;
                     SVCandidate& best_sv = sv_list[0].first;
                     std::string& aln_type = sv_list[0].second;
                     int64_t sv_start = std::get<0>(best_sv);
@@ -667,7 +667,7 @@ void SVCaller::detectSVsFromSplitReads(SVData& sv_calls, PrimaryMap& primary_map
                     }
 
                     // Add the best SV call
-                    std::cout << "Adding best SV call" << std::endl;
+                    // std::cout << "Adding best SV call" << std::endl;
                     sv_calls.add(supp_chr, sv_start, sv_end, best_sv_type, ".", aln_type, best_sv_genotype, best_likelihood);
                 }
                 
@@ -699,7 +699,7 @@ void SVCaller::detectSVsFromSplitReads(SVData& sv_calls, PrimaryMap& primary_map
                 // Determine which SV to keep based on HMM prediction likelihood
                 if (sv_list.size() == 1) {
                     // Just add the SV call
-                    std::cout << "Adding single SV call" << std::endl;
+                    // std::cout << "Adding single SV call" << std::endl;
                     SVCandidate& best_sv = sv_list[0].first;
                     std::string& aln_type = sv_list[0].second;
                     int64_t sv_start = std::get<0>(best_sv);