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FastBQSR
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compare: zzh:4f9fecf078144d5d74bde8fee1442603a1d65596
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3 changed files with 6 additions and 6 deletions
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2
CMakeLists.txt
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@ -5,6 +5,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread") # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
# set(CMAKE_BUILD_TYPE Debug) # set(CMAKE_BUILD_TYPE Debug)
# set(CMAKE_BUILD_TYPE Release) # set(CMAKE_BUILD_TYPE Release)
#add_definitions(-DSHOW_PERF) add_definitions(-DSHOW_PERF)
# add_definitions(-DSHOW_PERF=1) # add_definitions(-DSHOW_PERF=1)
add_subdirectory(src) add_subdirectory(src)

10
src/bqsr/apply_bqsr_entry.cpp
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@ -187,11 +187,11 @@ int SerialApplyBQSR(AuxVar &aux) {
recalibratedQuals[offset] = quantizedQualityScore; 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) { if (sam_write1(nsgv::gOutBamFp, nsgv::gOutBamHeader, bw->b) < 0) {
spdlog::error("failed writing sam record to \"{}\"", nsgv::gBqsrArg.OUTPUT_FILE.c_str()); spdlog::error("failed writing sam record to \"{}\"", nsgv::gBqsrArg.OUTPUT_FILE.c_str());

BIN
test/in_test.bam 100644
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