drop progress

gear-genomics · Aug 26, 2024 · 6e1f4d5 · 6e1f4d5
1 parent 28ebbc0
commit 6e1f4d5
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Showing 7 changed files with 0 additions and 17 deletions.
diff --git a/src/bed.h b/src/bed.h
@@ -3,7 +3,6 @@
 
 #include <boost/filesystem.hpp>
 #include <boost/multi_array.hpp>
-#include <boost/progress.hpp>
 #include <boost/date_time/posix_time/posix_time.hpp>
 #include <boost/unordered_map.hpp>
 #include <boost/algorithm/string.hpp>

diff --git a/src/blacklist.h b/src/blacklist.h
@@ -18,7 +18,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #ifdef OPENMP
 #include <omp.h>
@@ -110,10 +109,7 @@ namespace dicey
 
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
     std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "Blacklist mappability map" << std::endl;
-    boost::progress_display show_progress( nchr );
     for(uint32_t refIndex = 0; refIndex < nchr; ++refIndex) {
-      ++show_progress;
-
       // Load chromosome
       std::string seqname(faidx_iseq(fai, refIndex));
       int32_t sql = faidx_seq_len(fai, seqname.c_str());

diff --git a/src/chop.h b/src/chop.h
@@ -17,7 +17,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #ifdef OPENMP
 #include <omp.h>
@@ -345,7 +344,6 @@ namespace dicey
 
 	boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
 	std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "Chop reference" << std::endl;
-	boost::progress_display show_progress( nchr );
 
 	uint32_t index = 0;
 	boost::iostreams::filtering_ostream of1;
@@ -355,8 +353,6 @@ namespace dicey
 	  of1.push(boost::iostreams::file_sink(read1fq.c_str(), std::ios_base::out | std::ios_base::binary));
 	}
 	for(uint32_t refIndex = 0; refIndex < nchr; ++refIndex) {
-	  ++show_progress;
-
 	  // Load chromosome
 	  std::string seqname(faidx_iseq(fai, refIndex));
 	  int32_t sql = faidx_seq_len(fai, seqname.c_str());
@@ -416,7 +412,6 @@ namespace dicey
 
       boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
       std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "Chop reference" << std::endl;
-      boost::progress_display show_progress( nchr );
 
       uint32_t index = 0;
       boost::iostreams::filtering_ostream of1;
@@ -432,7 +427,6 @@ namespace dicey
 	of2.push(boost::iostreams::file_sink(read2fq.c_str(), std::ios_base::out | std::ios_base::binary));
       }
       for(uint32_t refIndex = 0; refIndex < nchr; ++refIndex) {
-	++show_progress;
 
 	// Load chromosome
 	std::string seqname(faidx_iseq(fai, refIndex));

diff --git a/src/hunter.h b/src/hunter.h
@@ -22,7 +22,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #include <nlohmann/json.hpp>
 

diff --git a/src/index.h b/src/index.h
@@ -20,7 +20,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 using namespace sdsl;
 

diff --git a/src/mapbam.h b/src/mapbam.h
@@ -23,7 +23,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #ifdef OPENMP
 #include <omp.h>
@@ -107,10 +106,8 @@ namespace dicey
 
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
     std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "Mappability" << std::endl;
-    boost::progress_display show_progress( hdr->n_targets );
     // Iterate chromosomes
     for(uint32_t refIndex = 0; refIndex < (uint32_t) hdr->n_targets; ++refIndex) {
-      ++show_progress;
       if ((c.hasChr) && (std::string(hdr->target_name[refIndex]) != c.chrom)) continue;
       if (chrNoData(c, refIndex, idx)) continue;
 

diff --git a/src/neighbors.h b/src/neighbors.h
@@ -18,7 +18,6 @@
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #include <sdsl/suffix_arrays.hpp>
 #include <htslib/faidx.h>