broadinstitute / viral-ngs / 227

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travis-ci-com

let scaffolder use ambiguous alignments when no unambiguous ones exist (#904)

When scaffolding contigs to a reference, if no unambiguous alignments cover a part of reference, let the scaffolder consider ambiguous ones, when all alignments mostly agree on the sequence.  The ambiguity can be the result of a misassembly, where the same reference part appears twice in a contig.   Also, in case of a repeat, dropping all ambiguous alignments could leave a hole in the assembly.

2490 of 4176 branches covered (59.63%)

36 of 36 new or added lines in 1 file covered. (100.0%)

7387 of 9886 relevant lines covered (74.72%)

0.96 hits per line