Corrupted record: Record contains invalid Cigar
Hi, timofey prodanov , thanks you develop the bam crate;
When I use following code try to read bam.
fn basebam_record_reader(bam_file: &str) {
let reader = BamReader::from_path(bam_file, 4).unwrap();
for record in reader {
let mut record = record.unwrap();
println!("record: {:?}", record);
// println!("name: {:?}", record.name());
// println!("cigar: {}",record.cigar());
// println!("record end: {}",record.calculate_end());
}
}
fn main(){
// read_header()
let test_bam_file = "infile.bam";
// write_bam();
basebam_record_reader(test_bam_file);
}
I got following error, when I run cargo run;
thread 'main' panicked at 'called Result::unwrap()on anErr value: Custom { kind: InvalidData, error: "Corrupted record: Record contains invalid Cigar" }', src/main.rs:44:33
The error line is the fourth line; I use samtools view, I can see the lines, I can't find any error;
C00113:38:HGJG3DMXY:1:1244:21242:28009_1:N:0:GACGTCAT+TCAACTGG 163 chrM 10 42 5M96S = 15 106 TCTATCACCCTATTAACCACTCACAAAAACTCTCCATACATTTAATATTTTCATCTAAAAAATATACACACAATAACATTACAAAACACTAAAACCAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF MD:Z:24G0G0G1G8G5G0G7G3G0G0G0G0G0G1G1G3G1G3G4G1G1G2G2G0G1G2G0G1G1 NM:i:29 RG:Z:sample20230307-B-C00113-B-WGBS-20230306-10_I1 XG:Z:GA XM:Z:........................zxh.h........h.....hh.......z...xhhhhh.h.h...z.z...h....h.z.h..z..xh.h..zx.h. XR:Z:GA
C00113:38:HGJG3DMXY:1:1244:21242:28009_1:N:0:GACGTCAT+TCAACTGG 83 chrM 15 42 101M = 10 -106 CACCCTATTAACCACTCACAAAAACTCTCCATACATTTAATATTTTCATCTAAAAAATATACACACAATAACATTACAAAACACTAAAACCAAAACACCCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:19G0G0G1G8G5G0G7G3G0G0G0G0G0G1G1G3G1G3G4G1G1G2G2G0G1G2G0G1G6 RG:Z:sample20230307-B-C00113-B-WGBS-20230306-10_I1 XG:Z:GA NM:i:29 XM:Z:...................zxh.h........h.....hh.......z...xhhhhh.h.h...z.z...h....h.z.h..z..xh.h..zx.h...... XR:Z:CT
C00113:38:HGJG3DMXY:2:2404:16504:16235_1:N:0:GACGTCAT+TCAACTGG 163 chrM 18 42 82M = 18 82 CCTATTAACCACTCACAAAAACTCTCCATACATTTAATATTTTCATCTAAAAAATATACACACAATAACATTACAAAACACT FFFFF:FFFFFFF:FFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:16G0G0G1G8G5G0G7G3G0G0G0G0G0G1G1G3G1G3G4G1G1G2G2 RG:Z:sample20230307-B-C00113-B-WGBS-20230306-10_I1 XG:Z:GA NM:i:23 XM:Z:................zxh.h........h.....hh.......z...xhhhhh.h.h...z.z...h....h.z.h..z.. XR:Z:GA
C00113:38:HGJG3DMXY:2:2404:16504:16235_1:N:0:GACGTCAT+TCAACTGG 83 chrM 18 42 82S = 18 -82 CCTATTAACCACTCACAAAAACTCTCCATACATTTAATATTTTCATCTAAAAAATATACACACAATAACATTACAAAACACT FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFF:FFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF::FF::F:F MD:Z:16G0G0G1G8G5G0G7G3G0G0G0G0G0G1G1G3G1G3G4G1G1G2G2 RG:Z:sample20230307-B-C00113-B-WGBS-20230306-10_I1 XG:Z:GA NM:i:23 XM:Z:................zxh.h........h.....hh.......z...xhhhhh.h.h...z.z...h....h.z.h..z.. XR:Z:CT