clang changes

Signed-off-by: AdityaPandeyCN <[email protected]>

Author: AdityaPandeyCN

benchmark/generate_sam_benchmark.cxx

@@ -2,19 +2,17 @@
 #include "generate_sam_benchmark.h"
 #include <cstdio>
 
-static void BM_GenerateSAM(benchmark::State& state) {
-    int num_reads = state.range(0);
-    for (auto _ : state) {
-        GenerateSAMFile("benchmark_temp.sam", num_reads);
-        std::remove("benchmark_temp.sam");
-    }
+static void BM_GenerateSAM(benchmark::State &state)
+{
+   int num_reads = state.range(0);
+   for (auto _ : state) {
+      GenerateSAMFile("benchmark_temp.sam", num_reads);
+      std::remove("benchmark_temp.sam");
+   }
 
-    state.counters["reads_per_second"] = benchmark::Counter(
-        num_reads, benchmark::Counter::kIsRate);
-    state.counters["bytes_per_second"] = benchmark::Counter(
-        num_reads * 200, benchmark::Counter::kIsRate);
+   state.counters["reads_per_second"] = benchmark::Counter(num_reads, benchmark::Counter::kIsRate);
+   state.counters["bytes_per_second"] = benchmark::Counter(num_reads * 200, benchmark::Counter::kIsRate);
 }
 
 BENCHMARK(BM_GenerateSAM)->Range(100, 10000);
 BENCHMARK_MAIN();
-

benchmark/region_query_benchmark.cxx

@@ -100,4 +100,3 @@ BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benc
 BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);
 
 BENCHMARK_MAIN();
-

inc/ramcore/SamToNTuple.h

@@ -16,4 +16,3 @@ void samtoramntuple_split_by_chromosome(const char *datafile, const char *output
                                         const std::vector<std::string> &only_chromosomes = {});
 
 #endif
-

src/ramcore/RAMNTupleView.cxx

@@ -1,7 +1,11 @@
 #include "ramcore/RAMNTupleView.h"
-#include <iostream>
+
+#include <cstdint>
 #include <cstring>
+#include <iostream>
 #include <limits>
+#include <string>
+
 #include <ROOT/RNTuple.hxx>
 #include <ROOT/RNTupleReader.hxx>
 #include <ROOT/RNTupleView.hxx>
@@ -20,16 +24,16 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
       printf("ramntupleview: failed to open file %s\n", file);
       return 0;
    }
-   
+
    std::string region = query;
    if (region.empty() || region == "*") {
-       stopwatch.Print();
-       return reader->GetNEntries();
+      stopwatch.Print();
+      return reader->GetNEntries();
    }
 
    TString rname;
    Int_t range_start = 1;
-   Int_t range_end = std::numeric_limits<Int_t>::max(); 
+   Int_t range_end = std::numeric_limits<Int_t>::max();
 
    int chrDelimiterPos = region.find(":");
    if (chrDelimiterPos == std::string::npos) {
@@ -53,22 +57,22 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
 
    auto refs = RAMNTupleRecord::GetRnameRefs();
    auto refid = refs->GetRefId(rname.Data());
-   
+
    if (refid < 0) {
-       if (rname.BeginsWith("chr")) {
-           TString stripped_rname = rname(3, rname.Length() - 3);
-           refid = refs->GetRefId(stripped_rname.Data());
-       }
-       if (refid < 0 && (rname == "chrM" || rname == "M")) {
-           refid = refs->GetRefId("MT");
-       }
+      if (rname.BeginsWith("chr")) {
+         TString stripped_rname = rname(3, rname.Length() - 3);
+         refid = refs->GetRefId(stripped_rname.Data());
+      }
+      if (refid < 0 && (rname == "chrM" || rname == "M")) {
+         refid = refs->GetRefId("MT");
+      }
    }
-   
+
    if (refid < 0) {
-       std::cerr << "Error: Reference name '" << rname.Data() << "' not found in file.\n";
-       return 0;
+      std::cerr << "Error: Reference name '" << rname.Data() << "' not found in file.\n";
+      return 0;
    }
-   
+
    auto index = RAMNTupleRecord::GetIndex();
    auto flagView = reader->GetView<uint16_t>("record.flag");
    auto refidView = reader->GetView<int32_t>("record.refid");
@@ -77,18 +81,18 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
 
    Long64_t count = 0;
    const Long64_t totalEntries = reader->GetNEntries();
-   
-   const int FLAG_FILTER = 0x904; 
+
+   const int FLAG_FILTER = 0x904;
    const Int_t rs0 = (range_start > 0) ? (range_start - 1) : 0;
    const Int_t re0 = (range_end > 0) ? (range_end - 1) : 0;
-   constexpr int kMaxRefSpanHeuristic = 10000; 
+   constexpr int kMaxRefSpanHeuristic = 10000;
 
    auto computeRefSpan = [](const std::vector<uint32_t> &cigarOps) -> int {
       int span = 0;
       for (uint32_t op : cigarOps) {
          int len = static_cast<int>(op >> 4);
          int code = static_cast<int>(op & 0xF);
-         
+
          if (code == 0 || code == 2 || code == 3 || code == 7 || code == 8) {
             span += len;
          }
@@ -97,22 +101,25 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
    };
 
    if (!index || index->Size() == 0) {
-      
+
       bool seenRef = false;
       for (auto i : reader->GetEntryRange()) {
          const auto flag = flagView(i);
-         if (flag & FLAG_FILTER) continue;
-         
+         if (flag & FLAG_FILTER)
+            continue;
+
          const auto curRef = refidView(i);
          if (curRef == refid) {
             seenRef = true;
          } else {
-            if (seenRef && curRef > refid) break;
+            if (seenRef && curRef > refid)
+               break;
             continue;
          }
          const auto curPos = posView(i);
-         if (curPos > re0) break;
-         
+         if (curPos > re0)
+            break;
+
          int read_start = curPos;
          if (read_start >= rs0) {
             count++;
@@ -124,29 +131,35 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
          const auto &cigarOps = cigarView(i);
          int refSpan = computeRefSpan(cigarOps);
          int read_end = (refSpan > 0) ? (read_start + refSpan - 1) : read_start;
-         
+
          if (read_start <= re0 && read_end >= rs0) {
             count++;
          }
       }
    } else {
-      
+
       auto start_entry = index->GetRow(refid, rs0);
-      
-      if (start_entry < 0) start_entry = index->GetRow(refid, 0);
-      if (start_entry < 0) start_entry = 0;
+
+      if (start_entry < 0)
+         start_entry = index->GetRow(refid, 0);
+      if (start_entry < 0)
+         start_entry = 0;
 
       for (Long64_t j = start_entry; j < totalEntries; j++) {
          const auto flag = flagView(j);
-         if (flag & FLAG_FILTER) continue;
-         
+         if (flag & FLAG_FILTER)
+            continue;
+
          const auto curRef = refidView(j);
-         if (curRef < refid) continue;
-         if (curRef > refid) break;
-         
+         if (curRef < refid)
+            continue;
+         if (curRef > refid)
+            break;
+
          const auto curPos = posView(j);
-         if (curPos > re0) break;
-         
+         if (curPos > re0)
+            break;
+
          int read_start = curPos;
          if (read_start >= rs0) {
             count++;
@@ -158,14 +171,14 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
          const auto &cigarOps = cigarView(j);
          int refSpan = computeRefSpan(cigarOps);
          int read_end = (refSpan > 0) ? (read_start + refSpan - 1) : read_start;
-         
+
          if (read_end >= rs0) {
             count++;
          }
       }
    }
 
    stopwatch.Print();
+   std::cout << "Found " << static_cast<long long>(count) << " records in region " << (query ? query : "") << std::endl;
    return count;
 }
-