BWA alignments were performed using the bwa aln command with options –n 1, −o 0, and –e 0 and bwa samse with option –n 4. When doing a second alignment, the customized reference was updated, if necessary, to contain one of the alleles at predicted heterozygous sites from the first alignment, sequences were aligned, and the alignments were filtered as before.
Finally, the tools based on Direct fragmentation do not directly exploit paired-end information; they fragment every read before the first alignment and find fusion candidates aligning those fragments to a genomic reference.
If the ratio of correctly aligned bases between any such alignment and the second alignment was >0.8 and the subject regions didn't overlap, then that part was considered to be ambiguously mapped.
Common devices used in the first alignment turns are collaborative completion and repetition of the elements of the prior turn, but alliances can also be initiated through non-verbal devices such as head-shakes.
The second alignment would increase the length of the road by 19.9 mile.
RIDOT eventually constructed the fourth alignment, with the freeway beginning north of the I-295 interchange and proceeding north to the border between Woonsocket and Cumberland.
The first alignment of the Route 92 Freeway, proposed in the 1950s, was to begin at an interchange with Interstate 95, known as the Somerset Freeway in the community of Skillman (in Montgomery Township).
US 20 was part of the first alignment of the Lincoln Highway in 1913 from the current SR 2 in Rolling Prairie to Elkhart, where the Lincoln Highway turned southeast on to current US 33.
Finally, the fourth alignment called for the freeway to begin just north of the Route 146 and I-295 interchange in Lincoln, with a northern route heading to either Downtown Woonsocket or the Cumberland–Woonsocket border.
