Merge pull request #147 from samtools/jc_int_test

Added test to check min/max values for i tag in SAM/BAM

src/tests/java/htsjdk/samtools/SamSpecIntTest.java

@@ -0,0 +1,97 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2014 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 htsjdk.samtools.util.CloserUtil;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class SamSpecIntTest {
+    private static final File SAM_INPUT = new File("testdata/htsjdk/samtools/aux.sam");
+    private static final File BAM_INPUT = new File("testdata/htsjdk/samtools/aux.bam");
+
+    @Test
+    public void testSamIntegers() throws IOException {
+        final List<String> errorMessages = new ArrayList<String>();
+        final SamReader samReader = SamReaderFactory.makeDefault().open(SAM_INPUT);
+        final File bamOutput = File.createTempFile("test", ".bam");
+        final File samOutput = File.createTempFile("test", ".sam");
+        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeWriter(samReader.getFileHeader(), true, samOutput, null);
+        final SAMFileWriter bamWriter = new SAMFileWriterFactory().makeWriter(samReader.getFileHeader(), true, bamOutput, null);
+
+        final SAMRecordIterator iterator = samReader.iterator();
+        while (iterator.hasNext()) {
+            try {
+                final SAMRecord rec = iterator.next();
+                samWriter.addAlignment(rec);
+                bamWriter.addAlignment(rec);
+            } catch (final Throwable e) {
+                System.out.println(e.getMessage());
+                errorMessages.add(e.getMessage());
+            }
+        }
+
+        CloserUtil.close(samReader);
+        samWriter.close();
+        bamWriter.close();
+        Assert.assertEquals(errorMessages.size(), 2);
+        bamOutput.deleteOnExit();
+        samOutput.deleteOnExit();
+    }
+
+    @Test
+    public void testBamIntegers() throws IOException {
+        final List<String> errorMessages = new ArrayList<String>();
+        final SamReader bamReader = SamReaderFactory.makeDefault().open(BAM_INPUT);
+        final File bamOutput = File.createTempFile("test", ".bam");
+        final File samOutput = File.createTempFile("test", ".sam");
+        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, samOutput, null);
+        final SAMFileWriter bamWriter = new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, bamOutput, null);
+        final SAMRecordIterator iterator = bamReader.iterator();
+        while (iterator.hasNext()) {
+            try {
+                final SAMRecord rec = iterator.next();
+                samWriter.addAlignment(rec);
+                bamWriter.addAlignment(rec);
+            } catch (final Throwable e) {
+                System.out.println(e.getMessage());
+                errorMessages.add(e.getMessage());
+            }
+        }
+
+        CloserUtil.close(bamReader);
+        samWriter.close();
+        bamWriter.close();
+        Assert.assertEquals(errorMessages.size(), 2);
+        bamOutput.deleteOnExit();
+        samOutput.deleteOnExit();
+    }
+
+}

testdata/htsjdk/samtools/aux.sam

@@ -0,0 +1,26 @@
+@HD	VN:1.4	SO:unsorted
+@SQ	SN:Sheila	LN:20
+@RG	ID:ID	SM:foo
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P0:i:0
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P1:i:127
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P2:i:128
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P3:i:255
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P4:i:256
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P5:i:32767
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P6:i:32768
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P7:i:65535
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P8:i:65536
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P9:i:2147483647
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	PA:i:2147483648
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	PB:i:4294967295
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P0:i:-0
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P1:i:-127
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P2:i:-128
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P3:i:-255
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P4:i:-256
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P5:i:-32767
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P6:i:-32768
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P7:i:-65535
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P8:i:-65536
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	P9:i:-2147483647
+Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	PA:i:-2147483648