ramntupleview refactor

.gitignore

@@ -3,10 +3,11 @@ ramexample.root
 *.log
 *.perf
 *.bam
+*.sam
+*.png
 *.bam.bai
 *.root
 *.root.idx
-*.png
 .ipynb_checkpoints/
 tmp/
 *.so

CMakeLists.txt

@@ -29,12 +29,14 @@ set(CMAKE_INSTALL_INCLUDEDIR include)
         inc/ramcore/SamParser.h
         inc/ramcore/SamToTTree.h
         inc/ramcore/SamToNTuple.h
+        inc/ramcore/RAMNTupleView.h
     SOURCES
         src/ttree/RAMRecord.cxx
         src/rntuple/RAMNTupleRecord.cxx
         src/ramcore/SamParser.cxx
         src/ramcore/SamToTTree.cxx
         src/ramcore/SamToNTuple.cxx
+        src/ramcore/RAMNTupleView.cxx
     LINKDEF
         inc/ttree/LinkDef.h
     DEPENDENCIES
@@ -67,3 +69,4 @@ if(RAMTOOLS_BUILD_TESTS)
     enable_testing()
     add_subdirectory(test)
 endif()
+

README.md

@@ -23,4 +23,3 @@ ROOT scripts to convert a SAM file to a RAM (ROOT Alignment/Map) file and to wor
     root [0] .x ramview.C("ramexample.root","chr1:10150-10300")
     root [1] .q
 ```
-

inc/ramcore/RAMNTupleView.h

@@ -0,0 +1,7 @@
+#ifndef RAMCORE_RAMNTUPLEVIEW_H
+#define RAMCORE_RAMNTUPLEVIEW_H
+
+void ramntupleview(const char *file, const char *query = "", bool cache = true, bool perfstats = false,
+                   const char *perfstatsfilename = "perf.root");
+
+#endif // RAMCORE_RAMNTUPLEVIEW_H

src/ramcore/RAMNTupleView.cxx

@@ -0,0 +1,87 @@
+#include "ramcore/RAMNTupleView.h"
+#include <iostream>
+#include <cstring>
+#include <ROOT/RNTuple.hxx>
+#include <ROOT/RNTupleReader.hxx>
+#include <ROOT/RNTupleView.hxx>
+#include <TStopwatch.h>
+#include <TString.h>
+#include "rntuple/RAMNTupleRecord.h"
+
+void ramntupleview(const char *file, const char *query, bool cache, bool perfstats, const char *perfstatsfilename)
+{
+   TStopwatch stopwatch;
+   stopwatch.Start();
+
+   auto reader = RAMNTupleRecord::OpenRAMFile(file);
+   if (!reader) {
+      printf("ramntupleview: failed to open file %s\n", file);
+      return;
+   }
+
+   std::string region = query;
+   int chrDelimiterPos = region.find(":");
+   if (chrDelimiterPos == std::string::npos) {
+      std::cerr << "Invalid region format. Use rname:start-end\n";
+      return;
+   }
+   TString rname = region.substr(0, chrDelimiterPos);
+   int rangeDelimiterPos = region.find("-", chrDelimiterPos);
+   if (rangeDelimiterPos == std::string::npos) {
+      std::cerr << "Invalid region format. Use rname:start-end\n";
+      return;
+   }
+   Int_t range_start = std::stoi(region.substr(chrDelimiterPos + 1, rangeDelimiterPos - chrDelimiterPos - 1));
+   Int_t range_end = std::stoi(region.substr(rangeDelimiterPos + 1));
+
+   auto refid = RAMNTupleRecord::GetRnameRefs()->GetRefId(rname.Data());
+   auto index = RAMNTupleRecord::GetIndex();
+
+   auto recordView = reader->GetView<RAMNTupleRecord>("record");
+
+   if (!index || index->Size() == 0) {
+      int count = 0;
+      for (auto i : reader->GetEntryRange()) {
+         const auto &rec = recordView(i);
+         if (rec.refid == refid && rec.pos >= range_start - 1 && rec.pos <= range_end - 1) {
+            count++;
+         }
+      }
+      printf("Found %d records in region %s\n", count, query);
+   } else {
+      auto start_entry = index->GetRow(refid, range_start);
+      auto end_entry = index->GetRow(refid, range_end);
+      if (start_entry < 0)
+         start_entry = 0;
+      if (end_entry < 0)
+         end_entry = reader->GetNEntries();
+
+      printf("ramntupleview: %s:%d (%lld) - %d (%lld)\n", rname.Data(), range_start, start_entry, range_end, end_entry);
+
+      for (; start_entry < end_entry; start_entry++) {
+         const auto &rec = recordView(start_entry);
+         int seqlen = rec.GetSEQLEN();
+         if (rec.pos + seqlen > range_start - 1) {
+            break;
+         }
+      }
+
+      Long64_t j;
+      int count = 0;
+      for (j = start_entry; j < end_entry; j++) {
+         count++;
+      }
+
+      while (j < reader->GetNEntries()) {
+         const auto &rec = recordView(j);
+         if (rec.pos >= range_end)
+            break;
+         count++;
+         j++;
+      }
+
+      printf("Found %d records in region %s\n", count, query);
+   }
+
+   stopwatch.Print();
+}

tools/CMakeLists.txt

@@ -14,7 +14,15 @@ ROOT_EXECUTABLE(samtoramntuple
         ROOT::ROOTNTuple
 )
 
-install(TARGETS samtoram samtoramntuple
+ROOT_EXECUTABLE(ramntupleview
+    ramntupleview.cxx
+    LIBRARIES
+        ramcore
+        ROOT::Core
+        ROOT::ROOTNTuple
+)
+
+install(TARGETS samtoram samtoramntuple ramntupleview
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
@@ -25,7 +33,6 @@ set(ROOT_MACROS
     ramrandom.cxx
     ramview.cxx
     ramview_no_index.cxx
-    ramntupleview.cxx
     parsetreestats.cxx
 )
 

tools/ramntupleview.cxx

@@ -1,90 +1,17 @@
+#include "ramcore/RAMNTupleView.h"
 #include <iostream>
-#include <cstring>
-#include <ROOT/RNTuple.hxx>
-#include <ROOT/RNTupleReader.hxx>
-#include <ROOT/RNTupleView.hxx>
-#include <TStopwatch.h>
-#include <TString.h>
-#include "rntuple/RAMNTupleRecord.h"
 
-void ramntupleview(const char *file, const char *query, bool cache = true, 
-                  bool perfstats = false, const char *perfstatsfilename = "perf.root")
+int main(int argc, char *argv[])
 {
-    TStopwatch stopwatch;
-    stopwatch.Start();
+   if (argc < 2) {
+      std::cerr << "Usage: " << argv[0] << " <file.root> [rname:start-end]\n";
+      std::cerr << "Example: " << argv[0] << " output.root chr1:1000-2000\n";
+      return 1;
+   }
 
-    auto reader = RAMNTupleRecord::OpenRAMFile(file);
-    if (!reader) {
-        printf("ramntupleview: failed to open file %s\n", file);
-        return;
-    }
+   const char *file = argv[1];
+   const char *region = (argc > 2) ? argv[2] : "";
 
-    std::string region = query;
-    int chrDelimiterPos = region.find(":");
-    if (chrDelimiterPos == std::string::npos) {
-        std::cerr << "Invalid region format. Use rname:start-end\n";
-        return;
-    }
-    TString rname = region.substr(0, chrDelimiterPos);
-    int rangeDelimiterPos = region.find("-", chrDelimiterPos);
-    if (rangeDelimiterPos == std::string::npos) {
-        std::cerr << "Invalid region format. Use rname:start-end\n";
-        return;
-    }
-    Int_t range_start = std::stoi(region.substr(chrDelimiterPos + 1, rangeDelimiterPos - chrDelimiterPos - 1));
-    Int_t range_end = std::stoi(region.substr(rangeDelimiterPos + 1));
-
-    auto refid = RAMNTupleRecord::GetRnameRefs()->GetRefId(rname.Data());
-    auto index = RAMNTupleRecord::GetIndex();
-
-    auto recordView = reader->GetView<RAMNTupleRecord>("record");
-
-    if (!index || index->Size() == 0) {
-
-        int count = 0;
-        for (auto i : reader->GetEntryRange()) {
-            const auto& rec = recordView(i);
-            if (rec.refid == refid && rec.pos >= range_start - 1 && rec.pos <= range_end - 1) {
-                count++;
-            }
-        }
-        printf("Found %d records in region %s\n", count, query);
-    } else {
-
-        auto start_entry = index->GetRow(refid, range_start);
-        auto end_entry = index->GetRow(refid, range_end);
-        if (start_entry < 0) start_entry = 0;
-        if (end_entry < 0) end_entry = reader->GetNEntries();
-
-        printf("ramntupleview: %s:%d (%lld) - %d (%lld)\n", 
-               rname.Data(), range_start, start_entry, range_end, end_entry);
-
-        for (; start_entry < end_entry; start_entry++) {
-            const auto& rec = recordView(start_entry);
-
-            int seqlen = rec.GetSEQLEN();
-            if (rec.pos + seqlen > range_start - 1) {
-                break;
-            }
-        }
-
-        Long64_t j;
-        int count = 0;
-        for (j = start_entry; j < end_entry; j++) {
-            count++;
-        }
-
-        while (j < reader->GetNEntries()) {
-            const auto& rec = recordView(j);
-            if (rec.pos >= range_end)
-                break;
-            count++;
-            j++;
-        }
-
-        printf("Found %d records in region %s\n", count, query);
-    }
-
-    stopwatch.Print();
+   ramntupleview(file, region);
+   return 0;
 }
-