add unit test for TestBwamemIdxstats (#93)

add unit test for TestBwamemIdxstats

Author: tomkinsc

read_utils.py

@@ -1370,10 +1370,11 @@ def minimap2_idxstats(inBam, refFasta, outBam=None, outStats=None,
 
     assert outBam or outStats, "Either outBam or outStats must be specified"
 
+    bam_aligned = util.file.mkstempfname('.aligned.bam')
     if outBam is None:
-        bam_aligned = mkstempfname('.aligned.bam')
+        bam_filtered = mkstempfname('.filtered.bam')
     else:
-        bam_aligned = outBam
+        bam_filtered = outBam
 
     samtools = tools.samtools.SamtoolsTool()
     mm2 = tools.minimap2.Minimap2()
@@ -1382,21 +1383,24 @@ def minimap2_idxstats(inBam, refFasta, outBam=None, outStats=None,
     shutil.copyfile(refFasta, ref_indexed)
 
     mm2.align_bam(inBam, ref_indexed, bam_aligned)
-
+    
     if filterReadsAfterAlignment:
         samtools.filter_to_proper_primary_mapped_reads(bam_aligned, 
                                                        bam_filtered, 
                                                        require_pairs_to_be_proper=not doNotRequirePairsToBeProper, 
                                                        reject_singletons=not keepSingletons)
+        os.unlink(bam_aligned)
     else:
-        bam_filtered = bam_aligned
+        shutil.move(bam_aligned, bam_filtered)
 
     if outStats is not None:
         samtools.idxstats(bam_filtered, outStats)
 
     if outBam is None:
         os.unlink(bam_filtered)
 
+    
+
 def parser_minimap2_idxstats(parser=argparse.ArgumentParser()):
     parser.add_argument('inBam', help='Input unaligned reads, BAM format.')
     parser.add_argument('refFasta', help='Reference genome, FASTA format, pre-indexed by Picard and Novoalign.')
@@ -1435,10 +1439,11 @@ def bwamem_idxstats(inBam, refFasta, outBam=None, outStats=None,
 
     assert outBam or outStats, "Either outBam or outStats must be specified"
 
+    bam_aligned = util.file.mkstempfname('.aligned.bam')
     if outBam is None:
-        bam_aligned = mkstempfname('.aligned.bam')
+        bam_filtered = mkstempfname('.filtered.bam')
     else:
-        bam_aligned = outBam
+        bam_filtered = outBam
 
     samtools = tools.samtools.SamtoolsTool()
     bwa = tools.bwa.Bwa()
@@ -1456,8 +1461,9 @@ def bwamem_idxstats(inBam, refFasta, outBam=None, outStats=None,
                                                        bam_filtered, 
                                                        require_pairs_to_be_proper=not doNotRequirePairsToBeProper, 
                                                        reject_singletons=not keepSingletons)
+        os.unlink(bam_aligned)
     else:
-        bam_filtered = bam_aligned
+        shutil.move(bam_aligned, bam_filtered)
 
     if outStats is not None:
         samtools.idxstats(bam_filtered, outStats)

test/unit/test_read_utils.py

@@ -48,6 +48,25 @@ def test_bwamem_idxstats(self):
         self.assertEqual(actual_count, self.samtools.count(outBam, opts=['-F', '4']))
         self.assertGreater(actual_count, 18000)
 
+    def test_bwamem_idxstats_with_filtering(self):
+        inBam = os.path.join(util.file.get_test_input_path(), 'G5012.3.testreads.bam')
+        outBam = util.file.mkstempfname('.bam', directory=self.tempDir)
+        outStats = util.file.mkstempfname('.stats.txt', directory=self.tempDir)
+        read_utils.bwamem_idxstats(inBam, self.ebolaRef, outBam, outStats, filterReadsAfterAlignment=True)
+        with open(outStats, 'rt') as inf:
+            actual_count = int(inf.readline().strip().split('\t')[2])
+        self.assertEqual(actual_count, self.samtools.count(outBam, opts=['-F', '4']))
+        self.assertLess(actual_count, 18000)
+
+        outBamNoFiltering = util.file.mkstempfname('.bam', directory=self.tempDir)
+        outStatsNoFiltering = util.file.mkstempfname('.stats.txt', directory=self.tempDir)
+        read_utils.bwamem_idxstats(inBam, self.ebolaRef, outBamNoFiltering, outStatsNoFiltering, filterReadsAfterAlignment=False)
+        with open(outStatsNoFiltering, 'rt') as inf:
+            count_without_filtering = int(inf.readline().strip().split('\t')[2])
+
+        # the filtered count should be less than the count without filtering
+        self.assertLess(actual_count, count_without_filtering)
+
     def test_bwamem_idxstats_no_bam_output(self):
         inBam = os.path.join(util.file.get_test_input_path(), 'G5012.3.testreads.bam')
         outStats = util.file.mkstempfname('.stats.txt', directory=self.tempDir)