Add toy SAM/BAM files, add test for bam_parser.parse_bam_header

CHANGELOG.md

@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 ### Added
 - Functional testing framework with concrete tests for `methods.set_env()`
+- Functional test for `bam_parser.parse_bam_header()`.
 
 ---
 

tests/BamParserTests.groovy

@@ -0,0 +1,52 @@
+import java.nio.file.Path
+import java.nio.file.Paths
+
+import static groovy.test.GroovyAssert.shouldFail
+
+import nextflow.util.ConfigHelper
+import org.junit.Test
+
+import validator.bl.NextflowConfigTests
+
+class BamParserTests extends NextflowConfigTests {
+    protected Path get_projectDir() {
+        return Paths.get(
+            getClass().protectionDomain.codeSource.location.path
+        ).getParent().getParent()
+    }
+
+    @Override
+    protected def generate_config_text(configobj) {
+        return """
+        includeConfig "\${projectDir}/config/bam/bam_parser.config"
+
+        ${ConfigHelper.toCanonicalString(configobj)}
+
+        params.header = bam_parser.parse_bam_header(params.bam_file)
+        """
+    }
+
+    @Test
+    void parse_missing_read_group() {
+        def bam_path = builder.get_launchDir().resolve("data/toy.bam").toString()
+        inconfig.params.bam_file = bam_path
+        expected.params.bam_file = bam_path
+        expected.params.header = [read_group: []]
+
+        compare()
+    }
+
+    @Test
+    void parse_read_group() {
+        def bam_path = builder.get_launchDir().resolve("data/toy-rg.bam").toString()
+        inconfig.params.bam_file = bam_path
+        expected.params.bam_file = bam_path
+        expected.params.header = [
+            read_group: [
+                [LB: 'lib1', ID: '4', PL: 'illumina', SM: '20', PU: 'unit1'],
+            ]
+        ]
+
+        compare()
+    }
+}

tests/data/README.md

@@ -0,0 +1,6 @@
+# Toy SAM / BAM Files
+This directory contains valid tiny files for testing.
+
+* `toy.sam` comes from the [samtools repository](https://github.com/samtools/samtools/blob/554bb9043a2da9ea5db85095dce21b742ba1fb71/examples/toy.sam).
+* `toy-rg.sam` is `toy.sam` with a manually-added `@RG` header line.
+* `toy.bam` and `toy-rg.bam` come from running `samtools view -bS XXX.sam > XXX.bam`.

tests/data/toy-rg.sam

@@ -0,0 +1,16 @@
+@SQ	SN:ref	LN:45
+@SQ	SN:ref2	LN:40
+@RG	ID:4	LB:lib1	PL:illumina	SM:20	PU:unit1
+@CO	https://github.com/samtools/samtools/blob/554bb9043a2da9ea5db85095dce21b742ba1fb71/examples/toy.sam
+r001	163	ref	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112
+r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*
+r003	0	ref	9	30	5H6M	*	0	0	AGCTAA	*
+r004	0	ref	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r003	16	ref	29	30	6H5M	*	0	0	TAGGC	*
+r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT	*
+x1	0	ref2	1	30	20M	*	0	0	aggttttataaaacaaataa	????????????????????
+x2	0	ref2	2	30	21M	*	0	0	ggttttataaaacaaataatt	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	ttataaaacAAATaattaagtctaca	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CaaaTaattaagtctacagagcaac	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	aaTaattaagtctacagagcaact	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	Taattaagtctacagagcaacta	???????????????????????

tests/data/toy.sam

@@ -0,0 +1,15 @@
+@CO	https://github.com/samtools/samtools/blob/554bb9043a2da9ea5db85095dce21b742ba1fb71/examples/toy.sam
+@SQ	SN:ref	LN:45
+@SQ	SN:ref2	LN:40
+r001	163	ref	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112
+r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*
+r003	0	ref	9	30	5H6M	*	0	0	AGCTAA	*
+r004	0	ref	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
+r003	16	ref	29	30	6H5M	*	0	0	TAGGC	*
+r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT	*
+x1	0	ref2	1	30	20M	*	0	0	aggttttataaaacaaataa	????????????????????
+x2	0	ref2	2	30	21M	*	0	0	ggttttataaaacaaataatt	?????????????????????
+x3	0	ref2	6	30	9M4I13M	*	0	0	ttataaaacAAATaattaagtctaca	??????????????????????????
+x4	0	ref2	10	30	25M	*	0	0	CaaaTaattaagtctacagagcaac	?????????????????????????
+x5	0	ref2	12	30	24M	*	0	0	aaTaattaagtctacagagcaact	????????????????????????
+x6	0	ref2	14	30	23M	*	0	0	Taattaagtctacagagcaacta	???????????????????????

tests/suite.groovy

@@ -4,7 +4,8 @@ import org.junit.runner.JUnitCore
 result = JUnitCore.runClasses \
     ExampleTests, \
     SetEnvTests, \
-    AlignMethodsTests
+    AlignMethodsTests, \
+    BamParserTests
 
 String message = "Ran: " + result.getRunCount() + ", Ignored: " + result.getIgnoreCount() + ", Failed: " + result.getFailureCount()
 if (result.wasSuccessful()) {