-
Notifications
You must be signed in to change notification settings - Fork 371
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add piped input tests for RevertSam, MergeBamAlignment (#1974)
- Loading branch information
1 parent
77f4b09
commit 142282a
Showing
3 changed files
with
98 additions
and
25 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,44 +1,111 @@ | ||
| package picard.sam; | ||
|
|
||
| import htsjdk.samtools.SamReader; | ||
| import htsjdk.samtools.SamReaderFactory; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.DataProvider; | ||
| import org.testng.annotations.Test; | ||
| import picard.cmdline.CommandLineProgramTest; | ||
|
|
||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.stream.StreamSupport; | ||
|
|
||
| import static picard.sam.MergeBamAlignmentTest.fasta; | ||
| import static picard.sam.MergeBamAlignmentTest.unmappedBam; | ||
|
|
||
| public class PipedDataTest { | ||
| private static final String classPath = "\"" + System.getProperty("java.class.path") + "\" "; | ||
| private static final String picardCommandlinePreamble = "java -classpath " + classPath + "picard.cmdline.PicardCommandLine "; | ||
| private static final String testBam = "testdata/picard/sam/test.bam"; | ||
|
|
||
| private String classPath = "\"" + System.getProperty("java.class.path") + "\" "; | ||
| /** | ||
| * Creates the command line argument to be used for piped (/dev/stdin) input tests. | ||
| * | ||
| * @param inputSAM the path to the input SAM file. | ||
| * @return commandline for ViewSam. | ||
| */ | ||
| private String getViewSamPicardCommand(final String inputSAM){ | ||
| return picardCommandlinePreamble + | ||
| "ViewSam " + | ||
| "I=" + inputSAM + " " + | ||
| "ALIGNMENT_STATUS=All " + | ||
| "PF_STATUS=All "; | ||
| } | ||
|
|
||
| @Test | ||
| public void testSortSam() { | ||
| String[] command = { | ||
| @DataProvider(name = "pipedInputTestData") | ||
| public Object[][] getPipedInputTestData() throws IOException { | ||
| // Note the trailing space in each string block. | ||
| // TODO: port ArgumentBuilder from GATK so this would not be necessary. | ||
| final File sortSamOutput = File.createTempFile("SortSam_pipe_test", "bam"); | ||
| sortSamOutput.deleteOnExit(); | ||
| final String[] sortSamCommand = { | ||
| "/bin/bash", | ||
| "-c", | ||
| "java -classpath " + | ||
| classPath + | ||
| "picard.cmdline.PicardCommandLine " + | ||
| "ViewSam " + | ||
| "I=testdata/picard/sam/test.bam " + | ||
| "ALIGNMENT_STATUS=All " + | ||
| "PF_STATUS=All " + | ||
| "| " + | ||
| "java -classpath " + | ||
| classPath + | ||
| "picard.cmdline.PicardCommandLine " + | ||
| "SortSam " + | ||
| "I=/dev/stdin " + | ||
| "O=/dev/null " + | ||
| "SORT_ORDER=queryname" | ||
| getViewSamPicardCommand(testBam) + | ||
| "| " + | ||
| picardCommandlinePreamble + | ||
| "SortSam " + | ||
| "SORT_ORDER=queryname " + | ||
| "I=/dev/stdin " + | ||
| "O=" + sortSamOutput.getAbsolutePath() | ||
| }; | ||
|
|
||
| final File revertSamOutput = File.createTempFile("RevertSam_pipe_test", "bam"); | ||
| revertSamOutput.deleteOnExit(); | ||
| final String[] revertSamCommand = { | ||
| "/bin/bash", | ||
| "-c", | ||
| getViewSamPicardCommand(testBam) + | ||
| "| " + | ||
| picardCommandlinePreamble + | ||
| "RevertSam " + | ||
| "I=/dev/stdin " + | ||
| "O=" + revertSamOutput.getAbsolutePath() | ||
| }; | ||
|
|
||
|
|
||
| // Only test the case where the "alignedBam" argument is /dev/stdin, which is the standard use case (bwa -> MergeBamAlignment). | ||
| // | ||
| // Note that the input aligned bam must be query-name sorted (as it would be if it's piped from bwa). | ||
| // MergeBamAlignment fails if the coordinate sorted aligned bam is given, after trying to query-name sort dynamically and failing to find the reference header items, | ||
| // seemingly due to the fact that the input is /dev/stdin. | ||
| final File mergeBamAlignmentOutput = File.createTempFile("MergeBamAlignment_pipe_test", "bam"); | ||
| mergeBamAlignmentOutput.deleteOnExit(); | ||
| final String[] mergeBamAlignmentCommand = { | ||
| "/bin/bash", | ||
| "-c", | ||
| getViewSamPicardCommand(MergeBamAlignmentTest.alignedQuerynameSortedBam.getAbsolutePath()) + // here we have to use "+", not ",". | ||
| "| " + | ||
| picardCommandlinePreamble + | ||
| "MergeBamAlignment " + | ||
| "ALIGNED_BAM=/dev/stdin " + | ||
| "UNMAPPED=" + unmappedBam + " " + | ||
| "REFERENCE_SEQUENCE=" + fasta + " " + | ||
| "OUTPUT=" + mergeBamAlignmentOutput.getAbsolutePath() | ||
| }; | ||
|
|
||
| return new Object[][]{ | ||
| {sortSamCommand, sortSamOutput}, | ||
| {revertSamCommand, revertSamOutput}, | ||
| {mergeBamAlignmentCommand, mergeBamAlignmentOutput} | ||
| }; | ||
| } | ||
|
|
||
| @Test(dataProvider = "pipedInputTestData") | ||
| public void testPipedInput(final String[] command, final File tmpOutput) { | ||
| try { | ||
| ProcessBuilder processBuilder = new ProcessBuilder(command); | ||
| processBuilder.inheritIO(); | ||
|
|
||
| Process process = processBuilder.start(); | ||
| Assert.assertEquals(process.waitFor(), 0); | ||
|
|
||
| final SamReader reader = SamReaderFactory.makeDefault().open(tmpOutput); | ||
| final long numOutputReads = StreamSupport.stream(reader.spliterator(), false).count(); | ||
| Assert.assertTrue(numOutputReads > 0); | ||
| Assert.assertTrue(reader.getFileHeader().getReadGroups().size() > 0); | ||
| } catch (Exception e) { | ||
| Assert.fail("Failed to pipe data from htsjdk to picard", e); | ||
| Assert.fail("Failed to pipe data to picard. The error was: ", e); | ||
| } | ||
| } | ||
| } |