From ea4671149f3054c773d99cea521db75bf7b0658f Mon Sep 17 00:00:00 2001
From: Yuri <yuri@rawbw.com>
Date: Mon, 30 Mar 2020 23:27:01 -0700
Subject: [PATCH] Fix the 'thread' C++ ambiguity by changing to boost::thread.

---
 src/cuffdiff.cpp  | 6 +++---
 src/cuffnorm.cpp  | 4 ++--
 src/cuffquant.cpp | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp
index 9ff8d157..773c5eb3 100644
--- a/src/cuffdiff.cpp
+++ b/src/cuffdiff.cpp
@@ -987,7 +987,7 @@ bool quantitate_next_locus(const RefSequenceTable& rt,
         
         if (pBundle->compatible_mass() > 0)
         {
-            thread quantitate(sample_worker,
+            boost::thread quantitate(sample_worker,
                               non_empty,
                               pBundle,
                               boost::ref(rt),
@@ -1715,7 +1715,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
         locus_curr_threads++;
         locus_thread_pool_lock.unlock();
         
-        thread inspect(inspect_map_worker,
+        boost::thread inspect(inspect_map_worker,
                        boost::ref(*fac),
                        boost::ref(tmp_min_frag_len),
                        boost::ref(tmp_max_frag_len),
@@ -1875,7 +1875,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
 				locus_curr_threads++;
 				locus_thread_pool_lock.unlock();
 				
-				thread bias(learn_bias_worker, fac);
+				boost::thread bias(learn_bias_worker, fac);
 #else
 				learn_bias_worker(fac);
 #endif
diff --git a/src/cuffnorm.cpp b/src/cuffnorm.cpp
index 1d2d7349..93129287 100644
--- a/src/cuffnorm.cpp
+++ b/src/cuffnorm.cpp
@@ -372,7 +372,7 @@ bool quantitate_next_locus(const RefSequenceTable& rt,
         
         if (pBundle->compatible_mass() > 0)
         {
-            thread quantitate(sample_worker,
+            boost::thread quantitate(sample_worker,
                               non_empty,
                               pBundle,
                               boost::ref(rt),
@@ -676,7 +676,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
         locus_curr_threads++;
         locus_thread_pool_lock.unlock();
         
-        thread inspect(inspect_map_worker,
+        boost::thread inspect(inspect_map_worker,
                        boost::ref(*fac),
                        boost::ref(tmp_min_frag_len),
                        boost::ref(tmp_max_frag_len),
diff --git a/src/cuffquant.cpp b/src/cuffquant.cpp
index 0018cc9b..c8ef9665 100644
--- a/src/cuffquant.cpp
+++ b/src/cuffquant.cpp
@@ -944,7 +944,7 @@ bool quantitate_next_locus(const RefSequenceTable& rt,
         locus_curr_threads++;
         locus_thread_pool_lock.unlock();
         
-        thread quantitate(sample_worker,
+        boost::thread quantitate(sample_worker,
                           boost::ref(rt),
                           boost::ref(*(bundle_factories[i])),
                           s_ab,
@@ -1157,7 +1157,7 @@ void driver(const std::string& ref_gtf_filename, const std::string& mask_gtf_fil
         locus_curr_threads++;
         locus_thread_pool_lock.unlock();
         
-        thread inspect(inspect_map_worker,
+        boost::thread inspect(inspect_map_worker,
                        boost::ref(*fac),
                        boost::ref(tmp_min_frag_len),
                        boost::ref(tmp_max_frag_len),
@@ -1306,7 +1306,7 @@ void driver(const std::string& ref_gtf_filename, const std::string& mask_gtf_fil
 				locus_curr_threads++;
 				locus_thread_pool_lock.unlock();
 				
-				thread bias(learn_bias_worker, fac);
+				boost::thread bias(learn_bias_worker, fac);
 #else
 				learn_bias_worker(fac);
 #endif