another testcase

rust-bio · Sep 17, 2024 · d5d3796 · d5d3796
1 parent 98fbdcd
commit d5d3796
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diff --git a/src/bam/record.rs b/src/bam/record.rs
@@ -2858,6 +2858,19 @@ mod alignment_cigar_tests {
         }
     }
 
+    #[test]
+    fn test_read_orientation_supplementary() {
+        let mut bam = Reader::from_path(&"test/test_orientation_supplementary.sam").unwrap();
+
+        for res in bam.records() {
+            let record = res.unwrap();
+            assert_eq!(
+                record.read_pair_orientation(),
+                SequenceReadPairOrientation::F2R1
+            );
+        }
+    }
+
     #[test]
     pub fn test_cigar_parsing_non_ascii_error() {
         let cigar_str = "43ጷ";

diff --git a/test/test_orientation_supplementary.sam b/test/test_orientation_supplementary.sam
@@ -0,0 +1,35 @@
+@HD	VN:1.3	SO:coordinate
+@SQ	SN:chr10	LN:135374737
+@SQ	SN:chr11	LN:134452384
+@SQ	SN:chr12	LN:132349534
+@SQ	SN:chr13	LN:114142980
+@SQ	SN:chr14	LN:106368585
+@SQ	SN:chr15	LN:100338915
+@SQ	SN:chr16	LN:88827254
+@SQ	SN:chr17	LN:78774742
+@SQ	SN:chr18	LN:76117153
+@SQ	SN:chr19	LN:63811651
+@SQ	SN:chr1	LN:247249719
+@SQ	SN:chr20	LN:62435964
+@SQ	SN:chr21	LN:46944323
+@SQ	SN:chr22	LN:49691432
+@SQ	SN:chr2	LN:242951149
+@SQ	SN:chr3	LN:199501827
+@SQ	SN:chr4	LN:191273063
+@SQ	SN:chr5	LN:180857866
+@SQ	SN:chr6	LN:170899992
+@SQ	SN:chr7	LN:158821424
+@SQ	SN:chr8	LN:146274826
+@SQ	SN:chr9	LN:140273252
+@SQ	SN:chrM	LN:16571
+@SQ	SN:chrX	LN:154913754
+@SQ	SN:chrY	LN:57772954
+@RG	ID:tumor	SM:tumor
+@PG	ID:bwa	PN:bwa	VN:0.7.16a-r1187-dirty	CL:resources/bwa mem -t 8 -Y -R @RG\tID:tumor\tSM:tumor index/hg18/genome reads/simulated.tumor.1.fastq reads/simulated.tumor.2.fastq
+@PG	ID:samtools	PN:samtools	PP:bwa	VN:1.20	CL:samtools sort -n -o tests/resources/testcases/test16/tumor.bam.namesorted.bam tests/resources/testcases/test16/tumor.bam
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.20	CL:samtools fixmate tests/resources/testcases/test16/tumor.bam.namesorted.bam tests/resources/testcases/test16/tumor.bam.fixed.bam
+@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.20	CL:samtools sort -o tests/resources/testcases/test16/tumor.bam tests/resources/testcases/test16/tumor.bam.fixed.bam
+@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.20	CL:samtools view -H tumor.bam
+sim_Som2-5-1_chr1_1_1b5889	163	chr1	938	60	100M	=	1143	264	CACTATACCACTTGAATGCTCAGAAGAAAAAAAAAAGAATTCAGAATATGTGTATTAAAATGGGTACAATAATGAGTAAAAAACTTGAAAGAAGCTGGAG	GFGDECGFE?AA>FGADEEF)BDC>FDEC5EEBFEEB?D@BGDCAB:FBGGDE;DF-CBDDCD+>:ED@#?=?#>EADE,B#?A#FFC;CC@#:5DBA##	NM:i:1	MD:Z:69A30	AS:i:95	XS:i:23	ZT:Z:95,1,72,72,0,0,69,0,1,0,0,0,1379,0	RG:Z:tumor	MQ:i:60	MC:Z:59M41S
+sim_Som2-5-1_chr1_1_1b5889	83	chr1	1143	60	59M41S	=	938	-264	ATCTTTCCTTTATCAACTATTGGTGTTAACCTTTGATTATATTTTTGCATAAGCATACAAAATATTGATCTTTAATTATACTAAGGAATCAATAGCCAAA	F:##.##D#DFDA5D#*#:D?E7B?.>?GA>6?=CE:EEBEDAE=AF:5GF:G#ABGDGGAGEG=DAE?FF?GG7AGEG-BDEGDAGEDDEDF=>F5E*@	NM:i:2	MD:Z:2G13A42	AS:i:51	XS:i:20	SA:Z:chr1,73497948,-,58S42M,60,1;	ZT:Z:51,2,31,11,0,0,42,0,3,0,0,0,419,0	RG:Z:tumor	MQ:i:60	MC:Z:100M
+sim_Som2-5-1_chr1_1_1b5889	2131	chr1	1263	60	58S42M	=	938	-367	ATCTTTCCTTTATCAACTATTGGTGTTAACCTTTGATTATATTTTTGCATAAGCATACAAAATATTGATCTTTAATTATACTAAGGAATCAATAGCCAAA	F:##.##D#DFDA5D#*#:D?E7B?.>?GA>6?=CE:EEBEDAE=AF:5GF:G#ABGDGGAGEG=DAE?FF?GG7AGEG-BDEGDAGEDDEDF=>F5E*@	NM:i:1	MD:Z:40C1	MC:Z:100M	AS:i:40	XS:i:0	SA:Z:chr1,73497828,-,59M41S,60,2;	ZT:Z:40,1,40,40,0,0,40,0,0,0,0,0,400,0	RG:Z:tumor