getAlignmentRefs

1 auto pileUp = [
2     ReadAlignment(SeededAlignment(), SeededAlignment()), ReadAlignment(SeededAlignment())
3 ];
4 auto allAlignmentChains = pileUp.getAlignmentRefs();
5 
6 assert(allAlignmentChains.length == 3);
7 assert(pileUp[0][0].id == 0);
8 assert(pileUp[0][1].id == 0);
9 assert(pileUp[1][0].id == 0);
10 
11 allAlignmentChains[0].id = 1;
12 allAlignmentChains[1].id = 2;
13 allAlignmentChains[2].id = 3;
14 
15 assert(pileUp[0][0].id == 1);
16 assert(pileUp[0][1].id == 2);
17 assert(pileUp[1][0].id == 3);