Implementation of a SAMRecord comparator that matches samtools' queryname sort order.

src/main/java/htsjdk/samtools/SAMRecordQueryNameNaturalComparator.java

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+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * 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 NONINFRINGEMENT. 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 htsjdk.samtools;
+
+import java.io.Serializable;
+
+/**
+ * Comparator for natural "queryname" (i.e. SO:queryname SS:natural) ordering of SAMRecords.
+ */
+public class SAMRecordQueryNameNaturalComparator extends SAMRecordQueryNameComparator implements Serializable {
+    private static final long serialVersionUID = 1L;
+
+    /** Compares two strings in a "natural" order. */
+    protected int compare(final String a, final String b) {
+        final int lenA = a.length(), lenB = b.length();
+        int ia = 0, ib = 0;
+
+        while (ia < lenA && ib < lenB) {
+            final char chA = a.charAt(ia);
+            final char chB = b.charAt(ib);
+            final boolean aIsDigit = Character.isDigit(chA);
+            final boolean bIsDigit = Character.isDigit(chB);
+            ia += 1;
+            ib += 1;
+
+            if (aIsDigit && bIsDigit) {
+                long numA = Character.digit(chA, 10);
+                int digitsA = 1;
+                while (ia < lenA && Character.isDigit(a.charAt(ia))) {
+                    numA *= 10;
+                    numA += Character.digit(a.charAt(ia), 10);
+                    ia += 1;
+                    digitsA += 1;
+                }
+
+                long numB = Character.digit(chB, 10);
+                int digitsB = 1;
+                while (ib < lenB && Character.isDigit(b.charAt(ib))) {
+                    numB *= 10;
+                    numB += Character.digit(b.charAt(ib), 10);
+                    ib += 1;
+                    digitsB += 1;
+                }
+
+                int comp = Long.compare(numA, numB);
+                if (comp == 0) comp = digitsB - digitsA; // more leading zeros sorts first
+                if (comp != 0) return comp;
+            }
+            else {
+                final int comp = Character.compare(chA, chB);
+                if (comp != 0) return comp;
+            }
+        }
+
+        // The strings are equal until one or both are out of characters to difference
+        // is solely based on length
+        return lenA - lenB;
+    }
+
+    /**
+     * Less stringent compare method than the regular compare.  If the two records
+     * are equal enough that their ordering in a sorted SAM file would be arbitrary,
+     * this method returns 0.
+     *
+     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
+     */
+    @Override
+    public int fileOrderCompare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
+        return compare(samRecord1.getReadName(), samRecord2.getReadName());
+    }
+}

src/test/java/htsjdk/samtools/SAMRecordQueryNameNaturalComparatorTest.java

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+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2017 Daniel Gomez-Sanchez
+ *
+ * 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 NONINFRINGEMENT. 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 htsjdk.samtools;
+
+import htsjdk.HtsjdkTest;
+import htsjdk.samtools.util.CollectionUtil;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class SAMRecordQueryNameNaturalComparatorTest extends HtsjdkTest {
+    private final static SAMRecordQueryNameNaturalComparator COMPARATOR = new SAMRecordQueryNameNaturalComparator();
+
+    @Test
+    public void testCompareDifferentNames() throws Exception {
+        // Example names in order from the SAMv1 spec
+        final List<String> names = CollectionUtil.makeList(
+                "abc", "abc+5", "abc- 5", "abc.d", "abc03", "abc5",
+                "abc008", "abc08", "abc8", "abc17", "abc17.+",
+                "abc17.2", "abc17.d", "abc59", "abcd"
+        );
+        final List<String> sorted = names.stream().sorted(COMPARATOR::compare).collect(Collectors.toList());
+
+        Assert.assertEquals(sorted, names);
+    }
+
+}