Direct normalization of chromosome at resolution

src/hic/HiCGlobals.java

@@ -29,7 +29,7 @@
  * @since 11/25/14
  */
 public class HiCGlobals {
-    public static final String versionNum = "3.26.00";
+    public static final String versionNum = "3.27.00";
     public static final int writingVersion = 9;
     public static final int bufferSize = 2097152;
     public static int MAX_PEARSON_ZOOM = 50000;

src/hic/tools/clt/CLTFactory.java

@@ -66,6 +66,8 @@ public static JuiceboxCLT getCLTCommand(String cmd) {
             return new Sum();
         } else if (cmd.startsWith("addnorm")) {
             return new AddNorm();
+        } else if (cmd.startsWith("test") && cmd.contains("norm")) {
+            return new TestNorm();
         } else if (cmd.equals("bigwig")) {
             return new BigWig();
         } else if (cmd.equals("bintopairs")) {

src/hic/tools/clt/old/TestNorm.java

@@ -0,0 +1,120 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2020-2022 Rice University, Baylor College of Medicine, Aiden Lab
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
+ *  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ *  THE SOFTWARE.
+ */
+
+package hic.tools.clt.old;
+
+import hic.HiCGlobals;
+import hic.tools.clt.CommandLineParser;
+import hic.tools.clt.JuiceboxCLT;
+import hic.tools.utils.bigarray.BigContactList;
+import hic.tools.utils.norm.IntraNorms;
+import hic.tools.utils.norm.NormalizationCalculations;
+import javastraw.reader.Dataset;
+import javastraw.reader.DatasetReaderV2;
+import javastraw.reader.basics.Chromosome;
+import javastraw.reader.datastructures.ListOfFloatArrays;
+import javastraw.reader.type.HiCZoom;
+
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+
+
+public class TestNorm extends JuiceboxCLT {
+
+    private final String norm = "SCALE";
+    private int resolution = 1000;
+    private String file, name, output;
+
+    public TestNorm() {
+        super(getBasicUsage());
+    }
+
+    public static String getBasicUsage() {
+        return "testNorm [-k NORM] [--threads number] [--mthreads number] <input.hic> <chromosome> <resolution> <output>";
+    }
+
+    @Override
+    public void readArguments(String[] args, CommandLineParser parser) {
+        if (parser.getHelpOption() || args.length != 5) {
+            printUsageAndExit();
+        }
+
+        HiCGlobals.normThreads = updateNumberOfCPUThreads(parser, 10);
+
+        file = args[1];
+        name = args[2];
+        resolution = Integer.parseInt(args[3]);
+        output = args[4];
+    }
+
+    @Override
+    public void run() {
+        HiCGlobals.allowDynamicBlockIndex = false;
+
+        try {
+            DatasetReaderV2 reader = new DatasetReaderV2(file, false, false);
+            Dataset ds = reader.read();
+            HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion());
+
+            Chromosome chrom = ds.getChromosomeHandler().getChromosomeFromName(name);
+            HiCZoom zoom = new HiCZoom(resolution);
+            String stem = "NORM_" + chrom.getIndex() + "_" + zoom.getBinSize();
+
+            BigContactList ba = IntraNorms.getBigArrayFromAndClearCache(ds, chrom, zoom, 0);
+            System.out.println("Contacts loaded to RAM");
+            if (ba != null) {
+                NormalizationCalculations nc = new NormalizationCalculations(ba, zoom.getBinSize());
+                ListOfFloatArrays vc = nc.computeVC();
+                long s0 = System.nanoTime();
+                ListOfFloatArrays scale = nc.computeSCALE(vc, stem);
+                long s1 = System.nanoTime();
+                System.out.println("Overall time taken " + ((s1 - s0) * 1e-9) + " seconds");
+                export(scale, output);
+            }
+
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    private void export(ListOfFloatArrays scale, String output) {
+        PrintWriter out = null;
+        try {
+            out = new PrintWriter(new OutputStreamWriter(
+                    new BufferedOutputStream(new FileOutputStream(output)), StandardCharsets.UTF_8));
+            for (float[] row : scale.getValues()) {
+                for (float val : row) {
+                    out.println(val);
+                }
+            }
+        } catch (FileNotFoundException e) {
+            e.printStackTrace();
+        } finally {
+            if (out != null) {
+                out.flush();
+                out.close();
+            }
+        }
+    }
+}

src/hic/tools/utils/norm/NormVectorInfo.java

@@ -1,7 +1,7 @@
 /*
  * The MIT License (MIT)
  *
- * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
+ * Copyright (c) 2020-2022 Rice University, Baylor College of Medicine, Aiden Lab
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -32,7 +32,7 @@
 import java.util.List;
 import java.util.Map;
 
-class NormVectorInfo {
+public class NormVectorInfo {
 
     private final BigListOfByteWriters normVectorBuffers;
     private final List<NormalizationVectorIndexEntry> normVectorIndices;

src/hic/tools/utils/norm/NormalizationCalculations.java

@@ -73,7 +73,7 @@ public void fixBySumFactor(ListOfFloatArrays norm) {
      *
      * @return Normalization vector
      */
-    ListOfFloatArrays computeVC() {
+    public ListOfFloatArrays computeVC() {
         return ba.getRowSums();
     }