Update sviper and print sviper header to log.

seqan · Dec 1, 2019 · 4471d67 · 4471d67
1 parent 343fc21
commit 4471d67
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/SViper b/SViper
diff --git a/src/alignment.cpp b/src/alignment.cpp
@@ -221,8 +221,8 @@ bool AlignmentManager::load()
                 ++splitReadCount;
             }
         }
-
-        optionManager->setShortReadLength(running_sum / 1000000);
+        if (!this->isLongRead)
+            optionManager->setShortReadLength(static_cast<int>(std::round(running_sum / 1000000)));
 
         // dataset contains small number of reads
         if (this->maxAbInsSize < 0 && this->readsForMedInsEst.size() != 0)

diff --git a/src/calloption.hpp b/src/calloption.hpp
@@ -58,7 +58,7 @@ class CallOptionManager : seqan3::argument_parser
         int32_t priMethod;
         int32_t filterMethod;
         uint32_t threadCount{std::thread::hardware_concurrency()};
-        unsigned shortReadLength{0};
+        int shortReadLength{0};
         bool writeBreakpoint{false};
         bool reportFilteredResult{false};
         bool skipRankAggregation{false};
@@ -124,8 +124,8 @@ class CallOptionManager : seqan3::argument_parser
         bool getUseRankAggregation(void) { return !skipRankAggregation; }
         void setMinVote(int v) { this->minVote = v;}
         bool getPolishing(void) {return !skipPolishing; }
-        void setShortReadLength(uint32_t average) { this->shortReadLength = average; }
-        uint32_t getShortReadLength() { return this->shortReadLength; }
+        void setShortReadLength(int average) { this->shortReadLength = average; }
+        int getShortReadLength() { return this->shortReadLength; }
 
         // for split-read
         double getMinSplitReadSupport(void) { return minSplitReadSupport; }

diff --git a/src/vaquita.cpp b/src/vaquita.cpp
@@ -74,7 +74,7 @@ int callMain(int argc, char const ** argv)
 
     // Loading & extraction
     RUN_IF(doShortReads, result, "SHORT READ EVIDENCE EXTRACTION", alnMgr.load()); // TODO: segmentation fault if fails (need fix)
-    printTimeMessage("Estimated short read length is " + std::to_string(oMgr.getShortReadLength()));
+    if (doShortReads) printTimeMessage("Estimated short read length is " + std::to_string(oMgr.getShortReadLength()));
     if (!result && !doLongReads) return 3;
     RUN_IF(doLongReads, result, "LONG READ EVIDENCE EXTRACTION", alnMgrLR.load());
     if (!result) return 3;
@@ -159,7 +159,7 @@ int callMain(int argc, char const ** argv)
         options.mean_coverage_of_short_reads = avg_read_depth;
         options.mean_insert_size_of_short_reads = alnMgr.getInsMedian();
         options.stdev_insert_size_of_short_reads = alnMgr.getInsSD();
-        options.length_of_short_reads = static_cast<int>(oMgr.getShortReadLength());
+        options.length_of_short_reads = oMgr.getShortReadLength();
         sviper::input_output_information info{options};
         bpMgrLR.getReadDepth()->longReadDepthCalc();
         int lr_depth = static_cast<int>(std::round(bpMgrLR.getReadDepth()->getMedianDepth()));
@@ -170,6 +170,7 @@ int callMain(int argc, char const ** argv)
             !sviper::open_file_success(info.log_file, (info.cmd_options.output_prefix + ".log").c_str()))
             return 1;
 
+        sviper::print_log_header(options, info.log_file);
         // Prepare file hangles for parallel computing
         // -------------------------------------------------------------------------
         RUN(result, "SViper: PREP PARALLEL PROCESSING", sviper::prep_file_handles(info));