pub fn estimate<R: NamedBamReader>(bam: &mut R) -> Result<Self, Box<dyn Error>> {
        let mut properties = AlignmentProperties {
            insert_size: InsertSize::default(),
            max_del_cigar_len: 0,
            max_ins_cigar_len: 0,
            frac_max_softclip: 0.0,
        };

        let mut record = bam::Record::new();
        let mut tlens = Vec::new();
        let mut max_mapq = 0;
        let mut i = 0;
        while i <= 10000 {
            if !bam.read(&mut record) {
                break;
            }

            if record.is_unmapped() || record.is_duplicate() || record.is_quality_check_failed() {
                continue;
            }

            max_mapq = cmp::max(max_mapq, record.mapq());

            let is_regular = properties.update_max_cigar_ops_len(&record);

            if is_regular
                && !record.is_mate_unmapped()
                && record.is_first_in_template()
                && record.tid() == record.mtid()
                && record.mapq() > 0
            {
                // record insert size
                tlens.push(record.insert_size().abs() as f64);
            }

            i += 1;
        }

        let upper = tlens.percentile(95);
        let lower = tlens.percentile(5);
        let mut valid = tlens
            .into_iter()
            .filter(|l| *l <= upper && *l >= lower)
            .collect_vec();
        properties.insert_size.mean = valid.median();
        properties.insert_size.sd = valid.iter().std_dev();

        Ok(properties)
    }
/// Estimate `AlignmentProperties` from first 10000 fragments of bam file.
/// Only reads that are mapped, not duplicates and where quality checks passed are taken.
Estimate `AlignmentProperties` from first 10000 fragments of bam file.
Only reads that are mapped, not duplicates and where quality checks passed are taken.
Estimate ` AlignmentProperties ` from first 10000 fragments of bam file . Only reads that are mapped not duplicates and where quality checks passed are taken .
pub fn estimate<R: NamedBamReader>(bam: &mut R) -> Result<Self, Box<dyn Error>> {
        let mut properties = AlignmentProperties {
            insert_size: InsertSize::default(),
            max_del_cigar_len: 0,
            max_ins_cigar_len: 0,
            frac_max_softclip: 0.0,
        };
        let mut record = bam::Record::new();
        let mut tlens = Vec::new();
        let mut max_mapq = 0;
        let mut i = 0;
        while i <= 10000 {
            if !bam.read(&mut record) {
                break;
            }
            if record.is_unmapped() || record.is_duplicate() || record.is_quality_check_failed() {
                continue;
            }
            max_mapq = cmp::max(max_mapq, record.mapq());
            let is_regular = properties.update_max_cigar_ops_len(&record);
            if is_regular
                && !record.is_mate_unmapped()
                && record.is_first_in_template()
                && record.tid() == record.mtid()
                && record.mapq() > 0
            {
                // record insert size
                tlens.push(record.insert_size().abs() as f64);
            }
            i += 1;
        }
        let upper = tlens.percentile(95);
        let lower = tlens.percentile(5);
        let mut valid = tlens
            .into_iter()
            .filter(|l| *l <= upper && *l >= lower)
            .collect_vec();
        properties.insert_size.mean = valid.median();
        properties.insert_size.sd = valid.iter().std_dev();
        Ok(properties)
    }
pub fn estimate < R : NamedBamReader > ( bam : & mut R ) -> Result < Self , Box < dyn Error > > { let mut properties = AlignmentProperties { insert_size : InsertSize :: default ( ) , max_del_cigar_len : 0 , max_ins_cigar_len : 0 , frac_max_softclip : 0.0 , } ; let mut record = bam :: Record :: new ( ) ; let mut tlens = Vec :: new ( ) ; let mut max_mapq = 0 ; let mut i = 0 ; while i <= 10000 { if ! bam . read ( & mut record ) { break ; } if record . is_unmapped ( ) || record . is_duplicate ( ) || record . is_quality_check_failed ( ) { continue ; } max_mapq = cmp :: max ( max_mapq , record . mapq ( ) ) ; let is_regular = properties . update_max_cigar_ops_len ( & record ) ; if is_regular && ! record . is_mate_unmapped ( ) && record . is_first_in_template ( ) && record . tid ( ) == record . mtid ( ) && record . mapq ( ) > 0 { // record insert size tlens . push ( record . insert_size ( ) . abs ( ) as f64 ) ; } i += 1 ; } let upper = tlens . percentile ( 95 ) ; let lower = tlens . percentile ( 5 ) ; let mut valid = tlens . into_iter ( ) . filter ( | l | * l <= upper && * l >= lower ) . collect_vec ( ) ; properties . insert_size . mean = valid . median ( ) ; properties . insert_size . sd = valid . iter ( ) . std_dev ( ) ; Ok ( properties ) }
Estimate `AlignmentProperties` from first 10000 fragments of bam file.
Estimate ` AlignmentProperties ` from first 10000 fragments of bam file .
bam
&mut R
bam
&mut R