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refactor: improved readability for read orientation inference (#439)
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* refactor: improved readability for read orientation inference

* fmt

* another testcase
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@johanneskoester
johanneskoester authored Nov 12, 2024
1 parent fc8ab72 commit eaa045e
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Showing 4 changed files with 288 additions and 18 deletions.
0 .cargo/config → config.toml
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68 changes: 50 additions & 18 deletions src/bam/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1088,30 +1088,36 @@ impl Record {
return SequenceReadPairOrientation::None;
}

let (is_reverse, is_first_in_template, is_mate_reverse) = if self.pos() < self.mpos() {
// given record is the left one
let (pos_1, pos_2, fwd_1, fwd_2) = if self.is_first_in_template() {
(
self.is_reverse(),
self.is_first_in_template(),
self.is_mate_reverse(),
self.pos(),
self.mpos(),
!self.is_reverse(),
!self.is_mate_reverse(),
)
} else {
// given record is the right one
(
self.is_mate_reverse(),
self.is_last_in_template(),
self.is_reverse(),
self.mpos(),
self.pos(),
!self.is_mate_reverse(),
!self.is_reverse(),
)
};
match (is_reverse, is_first_in_template, is_mate_reverse) {
(false, false, false) => SequenceReadPairOrientation::F2F1,
(false, false, true) => SequenceReadPairOrientation::F2R1,
(false, true, false) => SequenceReadPairOrientation::F1F2,
(true, false, false) => SequenceReadPairOrientation::R2F1,
(false, true, true) => SequenceReadPairOrientation::F1R2,
(true, false, true) => SequenceReadPairOrientation::R2R1,
(true, true, false) => SequenceReadPairOrientation::R1F2,
(true, true, true) => SequenceReadPairOrientation::R1R2,

if pos_1 < pos_2 {
match (fwd_1, fwd_2) {
(true, true) => SequenceReadPairOrientation::F1F2,
(true, false) => SequenceReadPairOrientation::F1R2,
(false, true) => SequenceReadPairOrientation::R1F2,
(false, false) => SequenceReadPairOrientation::R1R2,
}
} else {
match (fwd_2, fwd_1) {
(true, true) => SequenceReadPairOrientation::F2F1,
(true, false) => SequenceReadPairOrientation::F2R1,
(false, true) => SequenceReadPairOrientation::R2F1,
(false, false) => SequenceReadPairOrientation::R2R1,
}
}
} else {
SequenceReadPairOrientation::None
Expand Down Expand Up @@ -2844,6 +2850,32 @@ mod alignment_cigar_tests {
}
}

#[test]
fn test_read_orientation_f2r1() {
let mut bam = Reader::from_path(&"test/test_nonstandard_orientation.sam").unwrap();

for res in bam.records() {
let record = res.unwrap();
assert_eq!(
record.read_pair_orientation(),
SequenceReadPairOrientation::F2R1
);
}
}

#[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";
Expand Down
203 changes: 203 additions & 0 deletions test/test_nonstandard_orientation.sam
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@HD VN:1.6 SO:coordinate
@SQ SN:1 LN:248956422
@SQ SN:10 LN:133797422
@SQ SN:11 LN:135086622
@SQ SN:12 LN:133275309
@SQ SN:13 LN:114364328
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@RG ID:chm SM:chm PL:ILLUMINA
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem -t 8 -R @RG\tID:chm\tSM:chm\tPL:ILLUMINA resources/genome.fasta results/merged/chm_R1.fastq.gz results/merged/chm_R2.fastq.gz
@PG ID:GATK ApplyBQSR VN:4.1.4.1 CL:ApplyBQSR --output results/recal/chm.sorted.bam --bqsr-recal-file /tmp/tmpuhppums6/recal_table.grp --input results/mapped/chm.sorted.bam --reference resources/genome.fasta --preserve-qscores-less-than 6 --use-original-qualities false --quantize-quals 0 --round-down-quantized false --emit-original-quals false --global-qscore-prior -1.0 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false PN:GATK ApplyBQSR
@PG ID:samtools PN:samtools PP:GATK ApplyBQSR VN:1.20 CL:samtools view -H chm.bam
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -b nonstandard_orientation.sam
@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h test_nonstandard_orientation.bam
HK35WCCXX160124:1:2117:25885:46859 163 1 231 46 113M38S = 351 271 CAACCTCAGTTGACTTGGGGGACAAGGCAGCAGGAGCACCAGACCCCTGCACCACCTCCTTCTGGGTGGGAGATGAGGCAGCAGGAGCACCAGGGCCCTTCACGACCTCTTTCCAGGTGGGGGGGGAGGGAGCAGGGGCAGGAGAGCGCGT =BB?BCBCABD@C@?D@AAABD@CB?B@C@ACABCAAC@BDAC@BCCCBBD@CD@CDCCCEC;BCCCBCCE?CCCBCDCECCECDDCCEA(.<BAADDBFCEA%C=DECEEFB</=C@################################# XA:Z:1,+26345079,15S108M28S,3;1,+26344930,19S102M30S,2; MC:Z:151M MD:Z:90A0G11A9 RG:Z:chm NM:i:3 AS:i:98 XS:i:93
HK35WCCXX160124:1:2117:25885:46859 83 1 351 49 151M = 231 -271 GGGATGAGGTAGCAGCGGCACCAGGGCCCTTCACAACCTCTTTTGAGGTGGGGGACGAGGCAGCAGGAGCACCAGACCCCTGCACCACCTCCTTCTGGGTGGGAGATGAGGCAGCAGGAGCACCAGGGCCCTTCACGACCTCTTTCCAGGT ##########################DA4ADCDCFDDCE;/BB.(10@DCB<CCC/1DCBBCBBDCCDBBCCB>:BBCBBDAABBABBACCADCBCBB?CBBA1BABAAA@@B@AABBAAACB?9BBABA@DDAC2BBBBCBCDBCCFA=? XA:Z:1,-26345048,17S134M,8; MC:Z:113M38S MD:Z:1C7C5G0A28G5T4A46G32A14 RG:Z:chm NM:i:9 AS:i:109 XS:i:94
35 changes: 35 additions & 0 deletions test/test_orientation_supplementary.sam
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@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

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