INNER CODE UNIT · C

strand

dpryan79/MethylDackel · common.c:138

    int strand = getStrand(b)-1;
    int i, lb, rb;
    uint8_t *qual = bam_get_qual(b);
    uint8_t *seq = bam_get_seq(b);

    if(b->core.flag & BAM_FREAD2) {
        lb = bounds[4*strand+2];
        rb = bounds[4*strand+3];
    } else {
        lb = bounds[4*strand];
        rb = bounds[4*strand+1];
    }

    lb = (lb<b->core.l_qseq) ? lb : b->core.l_qseq;

    //trim on the left
    if(lb) {
        for(i=0; i<lb; i++) {

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