同上

CMakeLists.txt

@@ -5,6 +5,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
 # set(CMAKE_BUILD_TYPE Debug)
 # set(CMAKE_BUILD_TYPE Release)
-add_definitions(-DSHOW_PERF)
+#add_definitions(-DSHOW_PERF)
 # add_definitions(-DSHOW_PERF=1)
 add_subdirectory(src)

src/bqsr/apply_bqsr_entry.cpp

@@ -187,11 +187,11 @@ int SerialApplyBQSR(AuxVar &aux) {
                 recalibratedQuals[offset] = quantizedQualityScore;
             }
 
-            fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
+            // fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
-            for (size_t si = 0; si < sd.read_len; ++si) {
+            // for (size_t si = 0; si < sd.read_len; ++si) {
-                fprintf(gf[4], "%d ", (int)recalibratedQuals[si]);
+            //     fprintf(gf[4], "%d ", (int)recalibratedQuals[si]);
-            }
+            // }
-            fprintf(gf[4], "\n");
+            // fprintf(gf[4], "\n");
 
             if (sam_write1(nsgv::gOutBamFp, nsgv::gOutBamHeader, bw->b) < 0) {
                 spdlog::error("failed writing sam record to \"{}\"", nsgv::gBqsrArg.OUTPUT_FILE.c_str());