Allow the use of getSAMString on SAMReadGroupRecord objects

src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java

@@ -23,13 +23,12 @@
  */
 package htsjdk.samtools;
 
+import javax.xml.bind.annotation.XmlTransient;
 import java.io.Serializable;
 import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Set;
 
-import javax.xml.bind.annotation.XmlTransient;
-
 /**
  * Base class for the various concrete records in a SAM header, providing uniform
  * access to the attributes.
@@ -113,4 +112,10 @@ protected int attributesHashCode() {
     @Override public String toString() {
         return getClass().getSimpleName() + this.mAttributes.toString();
     }
+
+    /**
+     * Returns the record in the SAM line-based text format.  Fields are
+     * separated by '\t' characters. The String is NOT terminated by '\n'.
+     */
+    abstract public String getSAMString();
 }

src/main/java/htsjdk/samtools/SAMFileHeader.java

@@ -358,9 +358,14 @@ public int hashCode() {
     public final SAMFileHeader clone() {
         final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
         codec.setValidationStringency(ValidationStringency.SILENT);
+        return codec.decode(new StringLineReader(getSAMString()), "SAMFileHeader.clone");
+    }
+
+    @Override
+    public String getSAMString() {
         final StringWriter stringWriter = new StringWriter();
-        codec.encode(stringWriter, this);
-        return codec.decode(new StringLineReader(stringWriter.toString()), "SAMFileHeader.clone");
+        new SAMTextHeaderCodec().encode(stringWriter, this);
+        return stringWriter.toString();
     }
 
     /** Little class to generate program group IDs */

src/main/java/htsjdk/samtools/SAMProgramRecord.java

@@ -131,4 +131,10 @@ public int hashCode() {
     Set<String> getStandardTags() {
         return STANDARD_TAGS;
     }
+
+
+    @Override
+    public String getSAMString() {
+        return new SAMTextHeaderCodec().getPGLine(this);
+    }
 }

src/main/java/htsjdk/samtools/SAMReadGroupRecord.java

@@ -163,5 +163,10 @@ public int hashCode() {
     Set<String> getStandardTags() {
         return STANDARD_TAGS;
     }
+
+    @Override
+    public String getSAMString() {
+      return new SAMTextHeaderCodec().getRGLine(this);
+    }
 }
 

src/main/java/htsjdk/samtools/SAMSequenceRecord.java

@@ -23,6 +23,9 @@
  */
 package htsjdk.samtools;
 
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlValue;
 import java.math.BigInteger;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -32,10 +35,6 @@
 import java.util.Set;
 import java.util.regex.Pattern;
 
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlValue;
-
 /**
  * Header information about a reference sequence.  Corresponds to @SQ header record in SAM text header.
  */
@@ -246,5 +245,10 @@ public String toString() {
                 getAssembly()
         );
     }
+
+    @Override
+    public String getSAMString() {
+        return new SAMTextHeaderCodec().getSQLine(this);
+    }
 }
 

src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java

@@ -429,22 +429,27 @@ private void println(final String s) {
     }
 
     private void writePGLine(final SAMProgramRecord programRecord) {
-        if (programRecord == null) {
-            return;
-        }
+        println(getPGLine(programRecord));
+    }
+
+    protected String getPGLine(final SAMProgramRecord programRecord) {
         final String[] fields = new String[2 + programRecord.getAttributes().size()];
         fields[0] = HEADER_LINE_START + HeaderRecordType.PG;
         fields[1] = SAMProgramRecord.PROGRAM_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + programRecord.getProgramGroupId();
         encodeTags(programRecord, fields, 2);
-        println(StringUtil.join(FIELD_SEPARATOR, fields));
+        return StringUtil.join(FIELD_SEPARATOR, fields);
     }
 
     private void writeRGLine(final SAMReadGroupRecord readGroup) {
-        final String[] fields = new String[2 + readGroup.getAttributes().size()];
-        fields[0] = HEADER_LINE_START + HeaderRecordType.RG;
-        fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId();
-        encodeTags(readGroup, fields, 2);
-        println(StringUtil.join(FIELD_SEPARATOR, fields));
+        println(getRGLine(readGroup));
+    }
+    
+    protected String getRGLine(final SAMReadGroupRecord readGroup) {
+      final String[] fields = new String[2 + readGroup.getAttributes().size()];
+      fields[0] = HEADER_LINE_START + HeaderRecordType.RG;
+      fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId();
+      encodeTags(readGroup, fields, 2);
+      return StringUtil.join(FIELD_SEPARATOR, fields);
     }
 
     private void writeHDLine(final boolean keepExistingVersionNumber) {
@@ -470,13 +475,17 @@ private void writeHDLine(final boolean keepExistingVersionNumber) {
     }
 
     private void writeSQLine(final SAMSequenceRecord sequenceRecord) {
+        println(getSQLine(sequenceRecord));
+    }
+
+    protected String getSQLine(final SAMSequenceRecord sequenceRecord) {
         final int numAttributes = sequenceRecord.getAttributes() != null ? sequenceRecord.getAttributes().size() : 0;
         final String[] fields = new String[3 + numAttributes];
         fields[0] = HEADER_LINE_START + HeaderRecordType.SQ;
         fields[1] = SAMSequenceRecord.SEQUENCE_NAME_TAG + TAG_KEY_VALUE_SEPARATOR + sequenceRecord.getSequenceName();
         fields[2] = SAMSequenceRecord.SEQUENCE_LENGTH_TAG + TAG_KEY_VALUE_SEPARATOR + Integer.toString(sequenceRecord.getSequenceLength());
         encodeTags(sequenceRecord, fields, 3);
-        println(StringUtil.join(FIELD_SEPARATOR, fields));
+        return StringUtil.join(FIELD_SEPARATOR, fields);
     }
 
     /**

src/test/java/htsjdk/samtools/SAMProgramRecordTest.java

@@ -0,0 +1,42 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2017 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 org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * Test for SAMReadGroupRecordTest
+ */
+public class SAMProgramRecordTest {
+
+    @Test
+    public void testGetSAMString() {
+        SAMProgramRecord r = new SAMProgramRecord("SW-eIV");
+        r.setProgramName("telnet");
+        r.setProgramVersion("0.17-40");
+        r.setCommandLine("telnet towel.blinkenlights.nl");
+        Assert.assertEquals("@PG\tID:SW-eIV\tPN:telnet\tVN:0.17-40\tCL:telnet towel.blinkenlights.nl", r.getSAMString());
+    }
+}

src/test/java/htsjdk/samtools/SAMReadGroupRecordTest.java

@@ -0,0 +1,42 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2017 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 org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * Test for SAMReadGroupRecordTest
+ */
+public class SAMReadGroupRecordTest {
+
+    @Test
+    public void testGetSAMString() {
+        SAMReadGroupRecord r = new SAMReadGroupRecord("rg1");
+        r.setSample("mysample");
+        r.setPlatform("ILLUMINA");
+        r.setDescription("my description");
+        Assert.assertEquals("@RG\tID:rg1\tSM:mysample\tPL:ILLUMINA\tDS:my description", r.getSAMString());
+    }
+}

src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java

@@ -0,0 +1,42 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2017 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 org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * Test for SAMReadGroupRecordTest
+ */
+public class SAMSequenceRecordTest {
+
+    @Test
+    public void testGetSAMString() {
+        SAMSequenceRecord r = new SAMSequenceRecord("chr5_but_without_a_prefix", 271828);
+        r.setSpecies("Psephophorus terrypratchetti");
+        r.setAssembly("GRCt01");
+        r.setMd5("7a6dd3d307de916b477e7bf304ac22bc");
+        Assert.assertEquals("@SQ\tSN:chr5_but_without_a_prefix\tLN:271828\tSP:Psephophorus terrypratchetti\tAS:GRCt01\tM5:7a6dd3d307de916b477e7bf304ac22bc", r.getSAMString());
+    }
+}