drtconway

Testing alignments with strobealign

Evaluating a new aligner is hard. There are many circumstances where there isn't a single "correct" answer, which makes it difficult to compare alignments from two tools. Or where alignments are nondeterministic, it is not easy to determine if the alignments from two runs are as good as each other.

To compare bwa mem with strobealign, we have taken a well known sample NA24385, with good quality, publicly available read data SRR11321731, sub-sampled it in a reproducible way, then aligned it with both tools.

drtconway

// A cut down abstraction of a parser.
//
template <typename T>
struct parser
{   
    T v;
    
    explicit parser(T t) : v(t) {}
    
    T eval() { return v; }

drtconway

function Deque() {
    var rev = []
    var fwd = []

    this.size = function() {
        return rev.length + fwd.length
    }

    this.push_front = function(itm) {
        rev.push(itm)